Question: Variant callers reporting different read depth on same alignment
0
gravatar for Lauren
2.2 years ago by
Lauren50
Lauren50 wrote:

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?

ADD COMMENTlink modified 2.2 years ago by Pierre Lindenbaum120k • written 2.2 years ago by Lauren50
1

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

ADD REPLYlink written 2.2 years ago by Devon Ryan90k

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

ADD REPLYlink written 2.2 years ago by WouterDeCoster39k
2
gravatar for Pierre Lindenbaum
2.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

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

ADD COMMENTlink written 2.2 years ago by Pierre Lindenbaum120k
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