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

bug

master
chaopower 2024-01-08 13:38:36 +08:00
parent 455c598d36
commit fd769afbc7
2 changed files with 7 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
wdl/alignment.wdl
View File

@ -165,18 +165,18 @@ workflow alignment {
read1=normal_r1,
read2=normal_r2
}
call markduplicates_picard as tumor_markduplicates_picard_control {
call markduplicates_picard as normal_markduplicates_picard_control {
input:
name=tumor,
name=normal,
ref=ref,
output_dir=output_dir,
sorted_bam=bwa_tumor_control.sorted_bam,
}
if (umi) {
call markduplicates_genecore as normal_markduplicates_genecore {
call markduplicates_genecore as tumor_markduplicates_genecore {
input:
name=normal,
name=tumor,
ref=ref,
output_dir=output_dir,
sorted_bam=bwa_normal_control.sorted_bam,
@ -184,9 +184,9 @@ workflow alignment {
}
if (!umi) {
call markduplicates_picard as normal_markduplicates_picard {
call markduplicates_picard as tumor_markduplicates_picard {
input:
name=normal,
name=tumor,
ref=ref,
output_dir=output_dir,
sorted_bam=bwa_normal_control.sorted_bam,

2
wdl/call_mutation.wdl
View File

@ -267,7 +267,7 @@ task mutation_calling_tissue_control {
vcf_add_tag_msi.pl ${output_dir}/mutation/${name}.raw.snp_indel.vcf ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf ${probe} t
vcf_filter.py -i ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf \
-o ${output_dir}/mutation/${name}.snp_indel.somatic.vcf \AF[0] > 3*FORMAT/AF[1]
-o ${output_dir}/mutation/${name}.snp_indel.somatic.vcf
-e 'INFO/STATUS="StrongSomatic" | ( INFO/STATUS="LikelySomatic" && FORMAT/AF[0] > 3*FORMAT/AF[1] )'
vcf_filter.py -i ${output_dir}/mutation/${name}.raw.snp_indel.vcf \