Remove --skip-header option from PrintSVEvidence

broadinstitute · Mar 31, 2022 · 49b4a7f · 49b4a7f
1 parent 8089fa4
commit 49b4a7f
Show file tree

Hide file tree

Showing 4 changed files with 1 addition and 5 deletions.
diff --git a/wdl/BAFTestChromosome.wdl b/wdl/BAFTestChromosome.wdl
@@ -113,7 +113,6 @@ task BAFTest {
  set -o pipefail
 
  java -Xmx~{java_mem_mb}M -jar ${GATK_JAR} PrintSVEvidence \
- --skip-header \
  --sequence-dictionary ~{ref_dict} \
  --evidence-file ~{baf_metrics} \
  -L "${chrom}:${start}-${end}" \

diff --git a/wdl/PETestChromosome.wdl b/wdl/PETestChromosome.wdl
@@ -217,7 +217,6 @@ task PETest {
 
  if [ -s region.merged.bed ]; then
  java -Xmx~{java_mem_mb}M -jar ${GATK_JAR} PrintSVEvidence \
- --skip-header \
  --sequence-dictionary ~{ref_dict} \
  --evidence-file ~{discfile} \
  -L region.merged.bed \

diff --git a/wdl/ResolveCpxSv.wdl b/wdl/ResolveCpxSv.wdl
@@ -345,7 +345,6 @@ task ResolvePrep {
 
  if [ -s regions.bed ]; then
  java -Xmx~{java_mem_mb}M -jar ${GATK_JAR} PrintSVEvidence \
- --skip-header \
  --sequence-dictionary ~{ref_dict} \
  --evidence-file $GS_PATH_TO_DISC_FILE \
  -L regions.bed \
@@ -355,7 +354,7 @@ task ResolvePrep {
  fi
 
  cat ${SLICE}.PE.txt \
- | awk '{ if ($1==$4 && $3==$6) print }' \
+ | awk '{ if ($0!~"#" && $1==$4 && $3==$6) print }' \
  | bgzip -c \
  > ${SLICE}.PE.txt.gz
  rm ${SLICE}.PE.txt

diff --git a/wdl/SRTestChromosome.wdl b/wdl/SRTestChromosome.wdl
@@ -218,7 +218,6 @@ task SRTest {
 
  if [ -s region.merged.bed ]; then
  java -Xmx~{java_mem_mb}M -jar ${GATK_JAR} PrintSVEvidence \
- --skip-header \
  --sequence-dictionary ~{ref_dict} \
  --evidence-file ~{splitfile} \
  -L region.merged.bed \