Dear BRASS developer(s), I ran BRASS through the cgpwgs docker (it runs in thee steps: input, cover and main), the final .annot.bedpe.gz has no variants but header lines. Looking at the intermediates files: groups.filtered.bedpe has around 700 variants but clean.bedpe has no variants. Looking at the log files, it says:
Skipping` Sanger_CGP_Brass_Implement_cover.normal.23 as previously successful
Skipping Sanger_CGP_Brass_Implement_cover.tumour.24 as previously successful
Skipping Sanger_CGP_Brass_Implement_cover.normal.24 as previously successful
No data survived filtering (split_filtered)
No data survived (tabix, vcf)
No data survived (tabix, bedpe)
Do you have any clues of why this would happen? What filtering was here running?
Dear BRASS developer(s), I ran BRASS through the cgpwgs docker (it runs in thee steps: input, cover and main), the final
.annot.bedpe.gzhas no variants but header lines. Looking at the intermediates files:groups.filtered.bedpehas around 700 variants butclean.bedpehas no variants. Looking at the log files, it says:Do you have any clues of why this would happen? What filtering was here running?