chaopower
/
pipeline
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

bug

master
chaopower 2024-01-12 15:44:01 +08:00
parent b4c9ee1186
commit f09c61762c
2 changed files with 12 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
codes/public/hotspot/hotspot_delins.bed
View File

@ -1,3 +1,3 @@
chr7 55242414 55242513 chr7 55242394 55242533
chr7 55248985 55249172 chr7 55248965 55249192
chr17 37880978 37881164 chr17 37880958 37881184

14
wdl/call_mutation.wdl
View File

@ -295,12 +295,16 @@ task hotspot {
fi fi
# hotspot # hotspot
vcf_filter.py \ # vcf_filter.py \
-i ${raw_vcf} \ # -i ${raw_vcf} \
-e 'INFO/AF[0] < ${threshold}' \ # -e 'INFO/AF[0] < ${threshold}' \
-o ${output_dir}/mutation/${name}.raw.hotspot.vcf # -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 \ -b $PUBLIC/hotspot/hotspot_delins.bed \
-o ${output_dir}/mutation/${name}.raw.hotspot.delins.vcf -o ${output_dir}/mutation/${name}.raw.hotspot.delins.vcf