Closed xingyaoc closed 1 year ago
Hi,
Seems no germline variants output found, could you send the ${OUTPUT_DIR}/run_clairs.log
to my email address(zxzheng@cs.hku.hk) for us to pinpoint the error?
Hi,
Thanks for the response! To give you a bit of context, I am testing ClairS on a random subset of split bams (30/3000 from each tumor and normal, then I merge the bam subset and pass it into ClairS). This is probably why very few variants are being found for both germline and somatic. I have attached the log file as requested.
Best, Xingyao
Hi, Xingyao,
Thanks for the logs. Some contigs did have no SNPs output owing to the small BAM size. We have fixed the error and please try to re-pull the docker image(You might need to remove your local image first using dcoker rmi hkubal/clairs:latest
)
Zhenxian
VCFs are not generated for contigs where no variants are found, which breaks
select_hetero_snp_for_phasing
. clairs_output/vcf contains these files:Errors pasted from some of
1_select_hetero_snp_for_phasing.log
: