select_hetero_snp_for_phasing breaks for contigs where no variants are found

[xingyaoc]

select_hetero_snp_for_phasing breaks for contigs where no variants are found

[zhengzhenxian]

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

[zhengzhenxian]

Hi,

Seems no germline variants output found, could you send the ${OUTPUT_DIR}/run_clairs.log to my email address([email protected]) for us to pinpoint the error?

[xingyaoc]

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