Question: Variant callers reporting different read depth on same alignment
0
gravatar for Lauren
20 months ago by
Lauren30
Lauren30 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 20 months ago by Pierre Lindenbaum115k • written 20 months ago by Lauren30
1

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

ADD REPLYlink written 20 months ago by Devon Ryan86k

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

ADD REPLYlink written 20 months ago by WouterDeCoster35k
2
gravatar for Pierre Lindenbaum
20 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k 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 20 months ago by Pierre Lindenbaum115k
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