diff --git a/codes/public/hotspot/hotspot_delins.bed b/codes/public/hotspot/hotspot_delins.bed index 4e48a74..6cc6ed5 100644 --- a/codes/public/hotspot/hotspot_delins.bed +++ b/codes/public/hotspot/hotspot_delins.bed @@ -1,3 +1,3 @@ -chr7 55242414 55242513 -chr7 55248985 55249172 -chr17 37880978 37881164 \ No newline at end of file +chr7 55242394 55242533 +chr7 55248965 55249192 +chr17 37880958 37881184 \ No newline at end of file diff --git a/wdl/call_mutation.wdl b/wdl/call_mutation.wdl index 9645af8..be8d16b 100755 --- a/wdl/call_mutation.wdl +++ b/wdl/call_mutation.wdl @@ -295,12 +295,16 @@ task hotspot { fi # hotspot - vcf_filter.py \ - -i ${raw_vcf} \ - -e 'INFO/AF[0] < ${threshold}' \ - -o ${output_dir}/mutation/${name}.raw.hotspot.vcf +# vcf_filter.py \ +# -i ${raw_vcf} \ +# -e 'INFO/AF[0] < ${threshold}' \ +# -o ${output_dir}/mutation/${name}.raw.hotspot.vcf - vcf_operations.py ${output_dir}/mutation/${name}.raw.hotspot.vcf \ +# vcf_operations.py ${output_dir}/mutation/${name}.raw.hotspot.vcf \ +# -b $PUBLIC/hotspot/hotspot_delins.bed \ +# -o ${output_dir}/mutation/${name}.raw.hotspot.delins.vcf + + vcf_operations.py ${raw_vcf} \ -b $PUBLIC/hotspot/hotspot_delins.bed \ -o ${output_dir}/mutation/${name}.raw.hotspot.delins.vcf