Annotate small indels with CADD scores #325
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jemten
reviewed
Apr 18, 2023
assets/cadd_to_vcf_header_-1.0-.txt
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| @@ -0,0 +1 @@ | |||
| ##INFO=<ID=CADD,Number=1,Type=Float,Description="The CADD relative score for this alternative."> | |||
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| ##INFO=<ID=CADD,Number=1,Type=Float,Description="The CADD relative score for this alternative."> | |
| ##INFO=<ID=CADD,Number=1,Type=Float,Description="PHRED-like scaled CADD score"> |
workflows/raredisease.nf
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| @@ -140,6 +141,9 @@ workflow RAREDISEASE { | |||
| } | |||
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| // Initialize all file channels including unprocessed vcf, bed and tab files | |||
| ch_cadd_header = Channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() | |||
| ch_cadd_scores = params.cadd_annotation ? Channel.fromPath(params.cadd_annotation).collect() | |||
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| ch_cadd_scores = params.cadd_annotation ? Channel.fromPath(params.cadd_annotation).collect() | |
| ch_cadd_annotations = params.cadd_annotation ? Channel.fromPath(params.cadd_annotation).collect() |
The scores haven't been computed yet
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or maybe ch_cadd_resources is better? You decide :)
workflows/raredisease.nf
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| @@ -401,6 +405,8 @@ workflow RAREDISEASE { | |||
| if (!params.skip_mt_analysis) { | |||
| ANALYSE_MT ( | |||
| ch_mapped.bam_bai, | |||
| ch_cadd_header, | |||
| ch_cadd_scores, | |||
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| ch_cadd_scores, | |
| ch_cadd_annotations, |
workflows/raredisease.nf
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| @@ -448,6 +454,8 @@ workflow RAREDISEASE { | |||
| ANNOTATE_SNVS ( | |||
| ch_vcf, | |||
| params.analysis_type, | |||
| ch_cadd_header, | |||
| ch_cadd_scores, | |||
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Suggested change
| ch_cadd_scores, | |
| ch_cadd_annotations, |
| ch_vcf // channel: [mandatory] [ val(meta), path(vcfs) ] | ||
| ch_index // channel: [mandatory] [ val(meta), path(tbis) ] | ||
| ch_header // channel: [mandatory] [ path(txt) ] | ||
| ch_cadd_scores // channel: [mandatory] [ path(dir) ] |
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Suggested change
| ch_cadd_scores // channel: [mandatory] [ path(dir) ] | |
| ch_cadd_annotations // channel: [mandatory] [ path(dir) ] |
subworkflows/local/annotate_snvs.nf
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| GATK4_SELECTVARIANTS.out.vcf | ||
| .combine(ANNOTATE_CADD.out.vcf.ifEmpty("null")) | ||
| .branch { it -> | ||
| selvar: it[2].equals("null") | ||
| return [it[0], it[1]] | ||
| cadd: !(it[2].equals("null")) | ||
| return [it[2], it[3]] | ||
| } |
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Could you explain this code a bit more
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PR checklist
This PR adds the functionality to annotate small indel with CADD scores.
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR> -stub).nextflow run . -profile test_one_sample,docker --outdir <OUTDIR> -stub).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).