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select_hetero_snp_for_phasing breaks for contigs where no variants are found #5
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Hi, Seems no germline variants output found, could you send the |
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 Zhenxian |
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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
:The text was updated successfully, but these errors were encountered: