Pipeline: minor fixes for panel mode

hartwigmedical · Nov 17, 2022 · a04bc73 · a04bc73
1 parent 73389ed
commit a04bc73
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Showing 4 changed files with 11 additions and 4 deletions.
diff --git a/pipeline/scripts/run_gripss_somatic b/pipeline/scripts/run_gripss_somatic
@@ -12,6 +12,7 @@ known_hotspot_file=$1 && shift
 pon_sv_file=$1 && shift
 pon_sgl_file=$1 && shift
 repeat_mask_file=$1 && shift
+target_regions_bed=$1 && shift
 
 if [[ ! -d "${output_dir}" ]]; then
   mkdir ${output_dir}
@@ -45,7 +46,7 @@ args="${args} -ref_genome ${ref_genome} \
   -output_dir ${output_dir}"
 
 if [ "${run_mode}" == "PANEL" ]; then
-  args="${args} -filter_sgls
+  args="${args} -target_regions_bed ${target_regions_bed} \
     -hard_min_tumor_qual 200 -min_qual_break_point 1000 -min_qual_break_end 1000"
 fi
 

diff --git a/pipeline/scripts/run_pave_somatic b/pipeline/scripts/run_pave_somatic
@@ -11,6 +11,7 @@ ref_genome=$1 && shift
 ensembl_dir=$1 && shift
 driver_gene_panel=$1 && shift
 pon_file=$1 && shift
+pon_artefact_file=$1 && shift
 mappability_bed=$1 && shift
 gnomad_path=$1 && shift
 
@@ -46,6 +47,9 @@ args="-sample ${sample_id} \
   -read_pass_only \
   -output_vcf_file ${pave_vcf}"
 
+if [ "${run_mode}" == "PANEL" ]; then
+  args="${args} -pon_artefact_file ${pon_artefact_file}"
+fi
 
 if [ "${ref_genome_version}" == "V37" ]; then
   args="${args} -gnomad_freq_file ${gnomad_path}"

diff --git a/pipeline/scripts/run_pipeline b/pipeline/scripts/run_pipeline
@@ -105,6 +105,7 @@ if [ "${ref_genome_version}" == "V37" ]; then
   germline_blacklist_bed=${resources_dir}/variants/KnownBlacklist.germline.37.bed
   germline_blacklist_vcf=${resources_dir}/variants/KnownBlacklist.germline.37.vcf.gz
   gnomad_path=${resources_dir}/variants/gnomad_variants_v37.csv.gz
+  pon_artefact_file=${resources_dir}/variants/PanelArtefacts.37.tsv.gz
 
   # SVs (for Gripss, Linx)
   sv_hotspot_file=${resources_dir}/sv/known_fusions.37.bedpe
@@ -151,6 +152,7 @@ else
   germline_blacklist_bed=${resources_dir}/variants/KnownBlacklist.germline.38.bed
   germline_blacklist_vcf=${resources_dir}/variants/KnownBlacklist.germline.38.vcf.gz
   gnomad_path=${resources_dir}/variants/gnomad/
+  pon_artefact_file=${resources_dir}/variants/PanelArtefacts.38.tsv.gz
 
   # SVs (for Gripss, Linx)
   sv_hotspot_file=${resources_dir}/sv/known_fusions.38.bedpe
@@ -244,7 +246,7 @@ ${scripts_dir}/run_pave_somatic ${pave_jar} \
   ${tumor_id}  \
   ${sage_vcf} ${pave_somatic_dir} ${pave_vcf} \
   ${run_mode} ${ref_genome_version} ${ref_genome} \
-  ${ensembl_dir} ${driver_gene_panel} ${somatic_pon_file} ${mappability_bed} ${gnomad_path} \
+  ${ensembl_dir} ${driver_gene_panel} ${somatic_pon_file} ${pon_artefact_file} ${mappability_bed} ${gnomad_path} \
 
 
 # Sage germline
@@ -297,7 +299,7 @@ ${scripts_dir}/run_gripss_somatic ${gripss_jar} \
   ${tumor_id}  ${reference_id} \
   ${gripss_somatic_dir} ${gridss_vcf} \
   ${run_mode} ${ref_genome_version} ${ref_genome} \
-  ${sv_hotspot_file} ${sv_pon_file} ${sgl_pon_file} ${repeat_mask_file} \
+  ${sv_hotspot_file} ${sv_pon_file} ${sgl_pon_file} ${repeat_mask_file} ${target_regions_definition} \
 
 
 if [ "${reference_id}" != "none" ]; then

diff --git a/pipeline/scripts/run_sage_somatic b/pipeline/scripts/run_sage_somatic
@@ -44,7 +44,7 @@ args="${args} -hotspots ${hotspots} \
   -write_bqr_data \
   -out ${sage_vcf}"
 
-if [ ! "${run_mode}" == "PANEL" ]; then
+if [ "${run_mode}" == "PANEL" ]; then
   args="${args} -hotspot_min_tumor_vaf 0.01 -hotspot_min_tumor_qual 150 -panel_min_tumor_qual 250 -high_confidence_min_tumor_qual 350 -low_confidence_min_tumor_qual 500"
 fi