Empty vcf with strelka
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10 months ago
NT ▴ 20

Hi,

I have run strelka tool for variant calling on some data (bam files) and it has worked. However, when I wanted to run it again (after one month) on a larger cohort (the same data with other data) I got as output empty VCFs: There is a VCF header but no calls. There is no error in the logs files so I can't find where is the problem.

I have uninstall and install Strelka tool and run it again but I git always the same results: empty VCFs with only header and no errors in the logs file.

is there a reason for this? Thank you for ur help.

strelka germline variant calling • 364 views
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Your post has some typos that make it hard to understand. Also, please show us the exact commands you ran.

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This is not reproducible and nothing one can answer without any kind of details or the commands you used. Check that all BAM files indeed contain reads, check all error and message logs, try to reproduce with the BAM files you used last time.

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