This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Variant callers reporting different read depth on same alignment

I generated two VCFs, one with freebayes and one with GATK on the same BAM file.

At one position, freebayes called an MNV. At the same position, GATK called an SNV. What confuses me is that the depths are different in the VCF file. for example,

freebayes called:

chr 9 35906602 C A,T 0/1 6,7,6:19

and GATK called:

chr 9 35906602 C A 0/1 8,7:21

This might be obvious, but I'm new to all this. How can two callers report different total read depths like this? And how would one caller report a higher reference than the other?

freebayes gatk variant annotation variant calling
• 2,966 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Lauren Lauren

And how does it look like in e.g. igv?

• 0 views • link
written by WouterDeCoster WouterDeCoster

It's quite likely that they have slightly different defaults for filtering.

• 0 views • link
written by Devon Ryan Devon Ryan

1 answer

What confuses me is that the depths are different in the VCF file. f

different tools use different treshold; for example GATK will not consider

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this