Closed sli0001 closed 2 months ago
Hi Song,
I'm sorry to say that I don't work in the field anymore so I won't be able to help you fix this bug. If you manage to debug and fix it by yourself, I would gladly accept a pull request to merge it into the main branch to help others as well!
Hi,
No problem, I will try debugging and let you know if I come across a fix. I'll close this off for now -- thanks for your quick response!
Hi,
I'm running smart-phase in explorative mode, specifying a hg19-aligned bam, vardict vcf, and a target bed file:
The .vcf from vardict didn't originally contain
##contig
in the header, but I have added it usingbcftools reheader
. I'm now getting this error:The previous
INTERVAL CONTIGS
(INTERVAL CONTIG: 1
...INTERVAL CONTIG: 13
) all ran successfully, but it seems to be failing at chromosome 14.What could be causing this error? Any insight to help troubleshoot would be greatly appreciated, thank you!
King regards, Song