Merge pull request #74 from dhspence/patch-3

Disabled triallelic filter in dragen command.
genome · Sep 19, 2022 · 08c0289 · 08c0289
2 parents 9d9a7b0 + a7e389f
commit 08c0289
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/MyeloseqHD.wdl b/MyeloseqHD.wdl
@@ -321,7 +321,7 @@ task dragen_align {
 
          /bin/mkdir ${LocalSampleDir} && \
          /bin/mkdir ${outdir} && \
-         /opt/edico/bin/dragen -r ${DragenRef} --tumor-fastq1 ${fastq1} --tumor-fastq2 ${fastq2} --RGSM-tumor ${SM} --RGID-tumor ${RG} --RGLB-tumor ${LB} --enable-map-align true --enable-sort true --enable-map-align-output true --vc-enable-umi-liquid true --vc-combine-phased-variants-distance 3 --gc-metrics-enable=true --qc-coverage-region-1 ${CoverageBed} --qc-coverage-reports-1 full_res --umi-enable true --umi-min-supporting-reads ${readfamilysize} --umi-correction-scheme=random --umi-enable-probability-model-merging=false --umi-fuzzy-window-size=0 --enable-variant-caller=true --vc-target-bed ${CoverageBed} --enable-sv true --sv-call-regions-bed ${CoverageBed} --sv-exome true --sv-output-contigs true --vc-somatic-hotspots ${Hotspot} --umi-metrics-interval-file ${CoverageBed} --read-trimmers=fixed-len --trim-r1-5prime=${default=1 TrimLen} --trim-r1-3prime=${default=1 TrimLen} --trim-r2-5prime=${default=1 TrimLen} --trim-r2-3prime=${default=1 TrimLen} --output-dir ${LocalSampleDir} --output-file-prefix ${Name} --output-format BAM &> ${log} && \
+         /opt/edico/bin/dragen -r ${DragenRef} --tumor-fastq1 ${fastq1} --tumor-fastq2 ${fastq2} --RGSM-tumor ${SM} --RGID-tumor ${RG} --RGLB-tumor ${LB} --enable-map-align true --enable-sort true --enable-map-align-output true --vc-enable-umi-liquid true --vc-combine-phased-variants-distance 3 --vc-enable-triallelic-filter false --gc-metrics-enable=true --qc-coverage-region-1 ${CoverageBed} --qc-coverage-reports-1 full_res --umi-enable true --umi-min-supporting-reads ${readfamilysize} --umi-correction-scheme=random --umi-enable-probability-model-merging=false --umi-fuzzy-window-size=0 --enable-variant-caller=true --vc-target-bed ${CoverageBed} --enable-sv true --sv-call-regions-bed ${CoverageBed} --sv-exome true --sv-output-contigs true --vc-somatic-hotspots ${Hotspot} --umi-metrics-interval-file ${CoverageBed} --read-trimmers=fixed-len --trim-r1-5prime=${default=1 TrimLen} --trim-r1-3prime=${default=1 TrimLen} --trim-r2-5prime=${default=1 TrimLen} --trim-r2-3prime=${default=1 TrimLen} --output-dir ${LocalSampleDir} --output-file-prefix ${Name} --output-format BAM &> ${log} && \
          /bin/mv ${log} ./ && \
          /bin/mv ${LocalSampleDir} ${dragen_outdir}
      }