mean depth is OK, but median depth is -2 for all sample
wym0072003 opened this issue · comments
As the title, for my 100 WGS samples, the mean depth in peddy.het_check.csv is ~ 10, but all median depth are -2. Meanwhile, the hom_ref_count is 0 for all sample in sex_check_new.csv. What's the possible reason causes these issues? Thanks.
can you share the html output via email? that will help me to determine what is happening.
were these samples called individually and then the VCFs merged after? if so, don't expect peddy, or any tool to work properly.
Yes, it is merged VCF. Why peddy is not available for merged file?
I found it might work on merged vcf when setting missing variants as homo REF.
I will email you html later, thank you.