but the actual --vcf-tumor-id QFEND286A1 would be NGS02QFEND268A3_NGS02QFEND268A3 , so a) it is not correctly resolved from the given information and b) somehow the last digit is changed. On further inspection it has turned out that in general the ids are completey swapped occasionally. I guess some channel magic doesn't work somewhere, i.e. here:
2) Freebayes vcfs did not work for me, but resulted in: Command error: [E::vcf_parse_format] Invalid character '.' in 'GQ' FORMAT field at chr1:10146 Error: VCF parse error
3) There is an unused bcftools stats module
Description of feature
I noticed a couple of things when testing with tumor-only samples:
1) The used
--vcf-tumor-id
is not correctly resolved:Sample sheet has:
QFEND268A3,QFEND268A3,
assample,tumor_id
. For some reason this is what is in the.command.sh
:but the actual
--vcf-tumor-id QFEND286A1
would beNGS02QFEND268A3_NGS02QFEND268A3
, so a) it is not correctly resolved from the given information and b) somehow the last digit is changed. On further inspection it has turned out that in general the ids are completey swapped occasionally. I guess some channel magic doesn't work somewhere, i.e. here:2) Freebayes vcfs did not work for me, but resulted in:
Command error: [E::vcf_parse_format] Invalid character '.' in 'GQ' FORMAT field at chr1:10146 Error: VCF parse error
3) There is an unusedbcftools stats
module