diff --git a/modules/nf-core/vcf2maf/environment.yml b/modules/nf-core/vcf2maf/environment.yml index 2d273cd05f5..bfe50913b91 100644 --- a/modules/nf-core/vcf2maf/environment.yml +++ b/modules/nf-core/vcf2maf/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::vcf2maf=1.6.21 - bioconda::ensembl-vep=106.1 + - bioconda::vcf2maf=1.6.21 diff --git a/modules/nf-core/vcf2maf/tests/main.nf.test b/modules/nf-core/vcf2maf/tests/main.nf.test new file mode 100644 index 00000000000..f17e7740ee6 --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/main.nf.test @@ -0,0 +1,76 @@ +nextflow_process { + name "Test vcf2maf" + process "VCF2MAF" + script "../main.nf" + + tag "modules" + tag "modules_nfcore" + tag "vcf2maf" + tag "untar" + + test("Run without VEP") { + config "./nextflow.config" + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true) + ] + input[1] = [ file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] + input[2] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.maf[0][1]).readLines()[5..131], + process.out.versions + ).match() }, + { assert path(process.out.versions[0]).readLines() == ['"VCF2MAF":', ' vcf2maf: 1.6.21', ' ensemblvep: 106.1'] } + ) + } + } + + test("Run with VEP"){ + tag "vcf2maf-withVEP" + config "./nextflow.withVEP.config" + + setup { + run("UNTAR") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ id:'test_genome_vep' ], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vep.tar.gz", checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true) + ] + input[1] = [ file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] + input[2] = UNTAR.out.untar.map { it[1] } + """ + } + } + + then{ + assertAll( + { assert process.success }, + { assert path(process.out.maf[0][1]).readLines().size() == 2 }, // no variants, only header lines + { assert path(process.out.versions[0]).readLines() == ['"VCF2MAF":', ' vcf2maf: 1.6.21', ' ensemblvep: 106.1'] } + ) + } + } +} diff --git a/modules/nf-core/vcf2maf/tests/main.nf.test.snap b/modules/nf-core/vcf2maf/tests/main.nf.test.snap new file mode 100644 index 00000000000..c81d6c6221f --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/main.nf.test.snap @@ -0,0 +1,143 @@ +{ + "Run without VEP": { + "content": [ + [ + "Unknown\t0\t.\tGRCh38\tchr22\t1955\t1955\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t.\t\t\t\t\t\t\t\t\t\t1955", + "Unknown\t0\t.\tGRCh38\tchr22\t1957\t1957\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTA\t.\t.\t\t\t\t\t\t\t\t\t\t1957", + "Unknown\t0\t.\tGRCh38\tchr22\t1958\t1958\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAA\t.\t.\t\t\t\t\t\t\t\t\t\t1958", + "Unknown\t0\t.\tGRCh38\tchr22\t1959\t1959\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t1959", + "Unknown\t0\t.\tGRCh38\tchr22\t1960\t1960\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAT\t.\t.\t\t\t\t\t\t\t\t\t\t1960", + "Unknown\t0\t.\tGRCh38\tchr22\t1962\t1962\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t1962", + "Unknown\t0\t.\tGRCh38\tchr22\t1963\t1963\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAT\t.\t.\t\t\t\t\t\t\t\t\t\t1963", + "Unknown\t0\t.\tGRCh38\tchr22\t1964\t1964\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATC\t.\t.\t\t\t\t\t\t\t\t\t\t1964", + "Unknown\t0\t.\tGRCh38\tchr22\t1965\t1965\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCT\t.\t.\t\t\t\t\t\t\t\t\t\t1965", + "Unknown\t0\t.\tGRCh38\tchr22\t1966\t1966\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t1966", + "Unknown\t0\t.\tGRCh38\tchr22\t1967\t1967\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGT\t.\t.\t\t\t\t\t\t\t\t\t\t1967", + "Unknown\t0\t.\tGRCh38\tchr22\t1982\t1982\t+\tTargeted_Region\tSNP\tA\tA\tG\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\trs7287620\t176.64\t\t\t\t\t\t\t\t\t\t1982", + "Unknown\t0\t.\tGRCh38\tchr22\t1983\t1983\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t1983", + "Unknown\t0\t.\tGRCh38\tchr22\t2103\t2103\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATC\t.\t.\t\t\t\t\t\t\t\t\t\t2103", + "Unknown\t0\t.\tGRCh38\tchr22\t2104\t2104\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCC\t.\t.\t\t\t\t\t\t\t\t\t\t2104", + "Unknown\t0\t.\tGRCh38\tchr22\t2105\t2105\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCT\t.\t.\t\t\t\t\t\t\t\t\t\t2105", + "Unknown\t0\t.\tGRCh38\tchr22\t2107\t2107\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCT\t.\t.\t\t\t\t\t\t\t\t\t\t2107", + "Unknown\t0\t.\tGRCh38\tchr22\t2108\t2108\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTC\t.\t.\t\t\t\t\t\t\t\t\t\t2108", + "Unknown\t0\t.\tGRCh38\tchr22\t2111\t2111\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCT\t.\t.\t\t\t\t\t\t\t\t\t\t2111", + "Unknown\t0\t.\tGRCh38\tchr22\t2114\t2114\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\t.\t.\t\t\t\t\t\t\t\t\t\t2114", + "Unknown\t0\t.\tGRCh38\tchr22\t2115\t2115\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t2115", + "Unknown\t0\t.\tGRCh38\tchr22\t2118\t2118\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t2118", + "Unknown\t0\t.\tGRCh38\tchr22\t2123\t2123\t+\tTargeted_Region\tSNP\tC\tC\tG\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGCG\t.\t33.97\t\t\t\t\t\t\t\t\t\t2123", + "Unknown\t0\t.\tGRCh38\tchr22\t2124\t2124\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCGC\t.\t.\t\t\t\t\t\t\t\t\t\t2124", + "Unknown\t0\t.\tGRCh38\tchr22\t2717\t2717\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t2717", + "Unknown\t0\t.\tGRCh38\tchr22\t2722\t2722\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGT\t.\t.\t\t\t\t\t\t\t\t\t\t2722", + "Unknown\t0\t.\tGRCh38\tchr22\t2723\t2723\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTT\t.\t.\t\t\t\t\t\t\t\t\t\t2723", + "Unknown\t0\t.\tGRCh38\tchr22\t2724\t2724\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTA\t.\t.\t\t\t\t\t\t\t\t\t\t2724", + "Unknown\t0\t.\tGRCh38\tchr22\t2725\t2725\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAA\t.\t.\t\t\t\t\t\t\t\t\t\t2725", + "Unknown\t0\t.\tGRCh38\tchr22\t2837\t2837\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATA\t.\t.\t\t\t\t\t\t\t\t\t\t2837", + "Unknown\t0\t.\tGRCh38\tchr22\t2838\t2838\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAA\t.\t.\t\t\t\t\t\t\t\t\t\t2838", + "Unknown\t0\t.\tGRCh38\tchr22\t2908\t2908\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAA\t.\t.\t\t\t\t\t\t\t\t\t\t2908", + "Unknown\t0\t.\tGRCh38\tchr22\t2909\t2909\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t2909", + "Unknown\t0\t.\tGRCh38\tchr22\t2910\t2910\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t2910", + "Unknown\t0\t.\tGRCh38\tchr22\t2911\t2911\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAC\t.\t.\t\t\t\t\t\t\t\t\t\t2911", + "Unknown\t0\t.\tGRCh38\tchr22\t2912\t2912\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACT\t.\t.\t\t\t\t\t\t\t\t\t\t2912", + "Unknown\t0\t.\tGRCh38\tchr22\t3120\t3120\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAC\t.\t.\t\t\t\t\t\t\t\t\t\t3120", + "Unknown\t0\t.\tGRCh38\tchr22\t3121\t3121\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACC\t.\t.\t\t\t\t\t\t\t\t\t\t3121", + "Unknown\t0\t.\tGRCh38\tchr22\t3122\t3122\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCC\t.\t.\t\t\t\t\t\t\t\t\t\t3122", + "Unknown\t0\t.\tGRCh38\tchr22\t3125\t3125\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAGA\t.\t.\t\t\t\t\t\t\t\t\t\t3125", + "Unknown\t0\t.\tGRCh38\tchr22\t3127\t3127\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATC\t.\t.\t\t\t\t\t\t\t\t\t\t3127", + "Unknown\t0\t.\tGRCh38\tchr22\t3140\t3140\t+\tTargeted_Region\tSNP\tA\tA\tG\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAG\t.\t37.31\t\t\t\t\t\t\t\t\t\t3140", + "Unknown\t0\t.\tGRCh38\tchr22\t3141\t3141\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAGT\t.\t.\t\t\t\t\t\t\t\t\t\t3141", + "Unknown\t0\t.\tGRCh38\tchr22\t3145\t3145\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t.\t\t\t\t\t\t\t\t\t\t3145", + "Unknown\t0\t.\tGRCh38\tchr22\t3191\t3191\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t3191", + "Unknown\t0\t.\tGRCh38\tchr22\t3192\t3192\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAG\t.\t.\t\t\t\t\t\t\t\t\t\t3192", + "Unknown\t0\t.\tGRCh38\tchr22\t3197\t3197\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3197", + "Unknown\t0\t.\tGRCh38\tchr22\t3201\t3201\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATT\t.\t.\t\t\t\t\t\t\t\t\t\t3201", + "Unknown\t0\t.\tGRCh38\tchr22\t3208\t3208\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAG\t.\t.\t\t\t\t\t\t\t\t\t\t3208", + "Unknown\t0\t.\tGRCh38\tchr22\t3210\t3210\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTA\t.\t.\t\t\t\t\t\t\t\t\t\t3210", + "Unknown\t0\t.\tGRCh38\tchr22\t3218\t3218\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t3218", + "Unknown\t0\t.\tGRCh38\tchr22\t3219\t3219\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t3219", + "Unknown\t0\t.\tGRCh38\tchr22\t3266\t3266\t+\tTargeted_Region\tSNP\tT\tT\tC\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\trs4008589\t481.06\t\t\t\t\t\t\t\t\t\t3266", + "Unknown\t0\t.\tGRCh38\tchr22\t3267\t3267\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTA\t.\t.\t\t\t\t\t\t\t\t\t\t3267", + "Unknown\t0\t.\tGRCh38\tchr22\t3303\t3303\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAC\t.\t.\t\t\t\t\t\t\t\t\t\t3303", + "Unknown\t0\t.\tGRCh38\tchr22\t3304\t3304\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACT\t.\t.\t\t\t\t\t\t\t\t\t\t3304", + "Unknown\t0\t.\tGRCh38\tchr22\t3305\t3305\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTA\t.\t.\t\t\t\t\t\t\t\t\t\t3305", + "Unknown\t0\t.\tGRCh38\tchr22\t3309\t3309\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTA\t.\t.\t\t\t\t\t\t\t\t\t\t3309", + "Unknown\t0\t.\tGRCh38\tchr22\t3310\t3310\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAG\t.\t.\t\t\t\t\t\t\t\t\t\t3310", + "Unknown\t0\t.\tGRCh38\tchr22\t3318\t3318\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGC\t.\t.\t\t\t\t\t\t\t\t\t\t3318", + "Unknown\t0\t.\tGRCh38\tchr22\t3321\t3321\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTA\t.\t.\t\t\t\t\t\t\t\t\t\t3321", + "Unknown\t0\t.\tGRCh38\tchr22\t3352\t3352\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTC\t.\t.\t\t\t\t\t\t\t\t\t\t3352", + "Unknown\t0\t.\tGRCh38\tchr22\t3355\t3355\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3355", + "Unknown\t0\t.\tGRCh38\tchr22\t3356\t3356\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTC\t.\t.\t\t\t\t\t\t\t\t\t\t3356", + "Unknown\t0\t.\tGRCh38\tchr22\t3366\t3366\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATT\t.\t.\t\t\t\t\t\t\t\t\t\t3366", + "Unknown\t0\t.\tGRCh38\tchr22\t3374\t3374\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAG\t.\t.\t\t\t\t\t\t\t\t\t\t3374", + "Unknown\t0\t.\tGRCh38\tchr22\t3375\t3375\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAGA\t.\t.\t\t\t\t\t\t\t\t\t\t3375", + "Unknown\t0\t.\tGRCh38\tchr22\t3376\t3376\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAT\t.\t.\t\t\t\t\t\t\t\t\t\t3376", + "Unknown\t0\t.\tGRCh38\tchr22\t3378\t3378\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCG\t.\t.\t\t\t\t\t\t\t\t\t\t3378", + "Unknown\t0\t.\tGRCh38\tchr22\t3379\t3379\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCGG\t.\t.\t\t\t\t\t\t\t\t\t\t3379", + "Unknown\t0\t.\tGRCh38\tchr22\t3382\t3382\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCA\t.\t.\t\t\t\t\t\t\t\t\t\t3382", + "Unknown\t0\t.\tGRCh38\tchr22\t3386\t3386\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGCA\t.\t.\t\t\t\t\t\t\t\t\t\t3386", + "Unknown\t0\t.\tGRCh38\tchr22\t3387\t3387\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAG\t.\t.\t\t\t\t\t\t\t\t\t\t3387", + "Unknown\t0\t.\tGRCh38\tchr22\t3391\t3391\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAC\t.\t.\t\t\t\t\t\t\t\t\t\t3391", + "Unknown\t0\t.\tGRCh38\tchr22\t3393\t3393\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t3393", + "Unknown\t0\t.\tGRCh38\tchr22\t3394\t3394\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGA\t.\t.\t\t\t\t\t\t\t\t\t\t3394", + "Unknown\t0\t.\tGRCh38\tchr22\t3395\t3395\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\t.\t.\t\t\t\t\t\t\t\t\t\t3395", + "Unknown\t0\t.\tGRCh38\tchr22\t3396\t3396\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAC\t.\t.\t\t\t\t\t\t\t\t\t\t3396", + "Unknown\t0\t.\tGRCh38\tchr22\t3397\t3397\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACC\t.\t.\t\t\t\t\t\t\t\t\t\t3397", + "Unknown\t0\t.\tGRCh38\tchr22\t3398\t3398\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCT\t.\t.\t\t\t\t\t\t\t\t\t\t3398", + "Unknown\t0\t.\tGRCh38\tchr22\t3399\t3399\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t3399", + "Unknown\t0\t.\tGRCh38\tchr22\t3400\t3400\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGA\t.\t.\t\t\t\t\t\t\t\t\t\t3400", + "Unknown\t0\t.\tGRCh38\tchr22\t3401\t3401\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAT\t.\t.\t\t\t\t\t\t\t\t\t\t3401", + "Unknown\t0\t.\tGRCh38\tchr22\t3402\t3402\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATT\t.\t.\t\t\t\t\t\t\t\t\t\t3402", + "Unknown\t0\t.\tGRCh38\tchr22\t3403\t3403\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3403", + "Unknown\t0\t.\tGRCh38\tchr22\t3404\t3404\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t.\t\t\t\t\t\t\t\t\t\t3404", + "Unknown\t0\t.\tGRCh38\tchr22\t3405\t3405\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGT\t.\t.\t\t\t\t\t\t\t\t\t\t3405", + "Unknown\t0\t.\tGRCh38\tchr22\t3406\t3406\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTT\t.\t.\t\t\t\t\t\t\t\t\t\t3406", + "Unknown\t0\t.\tGRCh38\tchr22\t3407\t3407\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3407", + "Unknown\t0\t.\tGRCh38\tchr22\t3409\t3409\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3409", + "Unknown\t0\t.\tGRCh38\tchr22\t3410\t3410\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3410", + "Unknown\t0\t.\tGRCh38\tchr22\t3411\t3411\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3411", + "Unknown\t0\t.\tGRCh38\tchr22\t3413\t3413\t+\tTargeted_Region\tSNP\tT\tT\tG\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t78.64\t\t\t\t\t\t\t\t\t\t3413", + "Unknown\t0\t.\tGRCh38\tchr22\t3414\t3414\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGA\t.\t.\t\t\t\t\t\t\t\t\t\t3414", + "Unknown\t0\t.\tGRCh38\tchr22\t3418\t3418\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t3418", + "Unknown\t0\t.\tGRCh38\tchr22\t3421\t3421\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCT\t.\t.\t\t\t\t\t\t\t\t\t\t3421", + "Unknown\t0\t.\tGRCh38\tchr22\t3422\t3422\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTA\t.\t.\t\t\t\t\t\t\t\t\t\t3422", + "Unknown\t0\t.\tGRCh38\tchr22\t3423\t3423\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAG\t.\t.\t\t\t\t\t\t\t\t\t\t3423", + "Unknown\t0\t.\tGRCh38\tchr22\t3632\t3632\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGCT\t.\t.\t\t\t\t\t\t\t\t\t\t3632", + "Unknown\t0\t.\tGRCh38\tchr22\t3633\t3633\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t3633", + "Unknown\t0\t.\tGRCh38\tchr22\t3635\t3635\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGGA\t.\t.\t\t\t\t\t\t\t\t\t\t3635", + "Unknown\t0\t.\tGRCh38\tchr22\t3636\t3636\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\t.\t.\t\t\t\t\t\t\t\t\t\t3636", + "Unknown\t0\t.\tGRCh38\tchr22\t3637\t3637\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAG\t.\t.\t\t\t\t\t\t\t\t\t\t3637", + "Unknown\t0\t.\tGRCh38\tchr22\t3645\t3645\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCC\t.\t.\t\t\t\t\t\t\t\t\t\t3645", + "Unknown\t0\t.\tGRCh38\tchr22\t4466\t4466\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAT\t.\t.\t\t\t\t\t\t\t\t\t\t4466", + "Unknown\t0\t.\tGRCh38\tchr22\t4488\t4488\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACT\t.\t.\t\t\t\t\t\t\t\t\t\t4488", + "Unknown\t0\t.\tGRCh38\tchr22\t4489\t4489\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTT\t.\t.\t\t\t\t\t\t\t\t\t\t4489", + "Unknown\t0\t.\tGRCh38\tchr22\t4494\t4494\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCA\t.\t.\t\t\t\t\t\t\t\t\t\t4494", + "Unknown\t0\t.\tGRCh38\tchr22\t4495\t4495\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAG\t.\t.\t\t\t\t\t\t\t\t\t\t4495", + "Unknown\t0\t.\tGRCh38\tchr22\t4499\t4499\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGGT\t.\t.\t\t\t\t\t\t\t\t\t\t4499", + "Unknown\t0\t.\tGRCh38\tchr22\t4500\t4500\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTT\t.\t.\t\t\t\t\t\t\t\t\t\t4500", + "Unknown\t0\t.\tGRCh38\tchr22\t4501\t4501\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t4501", + "Unknown\t0\t.\tGRCh38\tchr22\t4502\t4502\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t.\t\t\t\t\t\t\t\t\t\t4502", + "Unknown\t0\t.\tGRCh38\tchr22\t4503\t4503\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGG\t.\t.\t\t\t\t\t\t\t\t\t\t4503", + "Unknown\t0\t.\tGRCh38\tchr22\t4508\t4508\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGC\t.\t.\t\t\t\t\t\t\t\t\t\t4508", + "Unknown\t0\t.\tGRCh38\tchr22\t4576\t4576\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATG\t.\t.\t\t\t\t\t\t\t\t\t\t4576", + "Unknown\t0\t.\tGRCh38\tchr22\t4579\t4579\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\t.\t.\t\t\t\t\t\t\t\t\t\t4579", + "Unknown\t0\t.\tGRCh38\tchr22\t4580\t4580\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t4580", + "Unknown\t0\t.\tGRCh38\tchr22\t4583\t4583\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAGC\t.\t.\t\t\t\t\t\t\t\t\t\t4583", + "Unknown\t0\t.\tGRCh38\tchr22\t4585\t4585\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTC\t.\t.\t\t\t\t\t\t\t\t\t\t4585", + "Unknown\t0\t.\tGRCh38\tchr22\t4586\t4586\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t4586", + "Unknown\t0\t.\tGRCh38\tchr22\t4587\t4587\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAT\t.\t.\t\t\t\t\t\t\t\t\t\t4587", + "Unknown\t0\t.\tGRCh38\tchr22\t4598\t4598\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t4598", + "Unknown\t0\t.\tGRCh38\tchr22\t4599\t4599\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGA\t.\t.\t\t\t\t\t\t\t\t\t\t4599", + "Unknown\t0\t.\tGRCh38\tchr22\t4605\t4605\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGT\t.\t.\t\t\t\t\t\t\t\t\t\t4605", + "Unknown\t0\t.\tGRCh38\tchr22\t4606\t4606\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTC\t.\t.\t\t\t\t\t\t\t\t\t\t4606", + "Unknown\t0\t.\tGRCh38\tchr22\t4608\t4608\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAA\t.\t.\t\t\t\t\t\t\t\t\t\t4608" + ], + [ + "versions.yml:md5,a81fb1aa49b86f6c9c17e3158336d930" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-12T15:59:58.867897" + } +} \ No newline at end of file diff --git a/modules/nf-core/vcf2maf/tests/nextflow.config b/modules/nf-core/vcf2maf/tests/nextflow.config new file mode 100644 index 00000000000..1f0aad364a7 --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/nextflow.config @@ -0,0 +1,11 @@ +// config for running without VEP +params.species = "homo_sapiens" +params.build = "GRCh38" + +process { + container = "biocontainers/vcf2maf:1.6.21--hdfd78af_0" + conda = "bioconda::vcf2maf=1.6.21" + withName: 'VCF2MAF' { + ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep" + } +} \ No newline at end of file diff --git a/modules/nf-core/vcf2maf/tests/nextflow.withVEP.config b/modules/nf-core/vcf2maf/tests/nextflow.withVEP.config new file mode 100644 index 00000000000..0991b358b00 --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/nextflow.withVEP.config @@ -0,0 +1,9 @@ +// config for running with VEP +params.species = "homo_sapiens" +params.build = "GRCh38" + +process { + withName: 'VCF2MAF' { + ext.args = "--ncbi-build ${params.build} --species ${params.species}" + } +} diff --git a/modules/nf-core/vcf2maf/tests/tags.yml b/modules/nf-core/vcf2maf/tests/tags.yml new file mode 100644 index 00000000000..b0c967f4207 --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/tags.yml @@ -0,0 +1,2 @@ +vcf2maf: + - modules/nf-core/vcf2maf/** diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index c24e252ec57..c86fb134d75 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -16,9 +16,11 @@ if ("$PROFILE" == "singularity") { singularity.autoMounts = true } else if ("$PROFILE" == "conda") { conda.enabled = true + conda.useMicromamba = true } else if ("$PROFILE" == "mamba") { conda.enabled = true conda.useMamba = true + conda.useMicromamba = true } else if ("$PROFILE" == "podman") { podman.enabled = true podman.userEmulation = true diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index f10ddc6b929..83f3c37d11f 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -813,9 +813,9 @@ varlociraptor/callvariants: varlociraptor/preprocess: - modules/nf-core/varlociraptor/preprocess/** - tests/modules/nf-core/varlociraptor/preprocess/** -vcf2maf: - - modules/nf-core/vcf2maf/** - - tests/modules/nf-core/vcf2maf/** +vcflib/vcfbreakmulti: + - modules/nf-core/vcflib/vcfbreakmulti/** + - tests/modules/nf-core/vcflib/vcfbreakmulti/** verifybamid/verifybamid2: - modules/nf-core/verifybamid/verifybamid2/** - tests/modules/nf-core/verifybamid/verifybamid2/** diff --git a/tests/modules/nf-core/vcf2maf/main.nf b/tests/modules/nf-core/vcf2maf/main.nf deleted file mode 100644 index 8deed5cf74a..00000000000 --- a/tests/modules/nf-core/vcf2maf/main.nf +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { VCF2MAF } from '../../../../modules/nf-core/vcf2maf/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' - -workflow test_vcf2maf_no_vep { - - input_vcf = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) - ] - fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - - VCF2MAF ( input_vcf, fasta, [] ) -} - -workflow test_vcf2maf_vep { - - input_vcf = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) - ] - fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - vep_cache = [ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['vep_cache'], checkIfExists: true) ] - - vep_cache_unpacked = UNTAR(vep_cache).untar.map { it[1] } - VCF2MAF ( input_vcf, fasta, vep_cache_unpacked) -} diff --git a/tests/modules/nf-core/vcf2maf/nextflow.config b/tests/modules/nf-core/vcf2maf/nextflow.config deleted file mode 100644 index 5505d8ec1e4..00000000000 --- a/tests/modules/nf-core/vcf2maf/nextflow.config +++ /dev/null @@ -1,14 +0,0 @@ -params.species = "homo_sapiens" -params.build = "GRCh38" - -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'test_vcf2maf_no_vep:VCF2MAF' { - ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep" - container = "biocontainers/vcf2maf:1.6.21--hdfd78af_0" - } - withName: 'test_vcf2maf_vep:VCF2MAF' { - ext.args = "--ncbi-build ${params.build} --species ${params.species}" - } -} diff --git a/tests/modules/nf-core/vcf2maf/test.yml b/tests/modules/nf-core/vcf2maf/test.yml deleted file mode 100644 index e62e39f8e43..00000000000 --- a/tests/modules/nf-core/vcf2maf/test.yml +++ /dev/null @@ -1,15 +0,0 @@ -- name: vcf2maf test_vcf2maf_no_vep - command: nextflow run ./tests/modules/nf-core/vcf2maf -entry test_vcf2maf_no_vep -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcf2maf/nextflow.config - tags: - - vcf2maf - files: - - path: output/vcf2maf/test.maf - md5sum: c7f357efa774fd5c4003d84f05212ed0 - -- name: vcf2maf test_vcf2maf_vep - command: nextflow run ./tests/modules/nf-core/vcf2maf -entry test_vcf2maf_vep -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcf2maf/nextflow.config - tags: - - vcf2maf - files: - - path: output/vcf2maf/test.maf - md5sum: bf114692a2f421225926c9b651eff161