Question: Inconsistency of allele depth in BAM and VCF
gravatar for CY
19 months ago by
United States
CY460 wrote:

We checked several alleles (locus) in both bam and vcf file. Almost all of them show a little bit high depth in bam file and a bit lower depth (AD) in vcf file. I guess this have something to do with variant caller filtering out some reads based on pre-defined criteria before make the variant calling.

Am I guessing right? If it is, what criteria probably are is this case? Base quality or something else?

bam variant allele depth vcf • 558 views
ADD COMMENTlink modified 19 months ago by Noushin N560 • written 19 months ago by CY460


the differences might come from how the variant caller works and how you calculate the read depth in the bam file. You have to tell us what variant caller you use and how do you calculate read depth. Than one can say more.

fin swimmer

ADD REPLYlink written 19 months ago by finswimmer13k

I used Metect basically with default parameters.

ADD REPLYlink written 19 months ago by CY460
gravatar for Noushin N
19 months ago by
Noushin N560
Baltimore, MD
Noushin N560 wrote:

You are right about the likely reason of this discrepancy. Essentially, you have to compare the filters used in the utility you are using for bam review (e.g. samtools) and the variant caller.

A few choices are:

  • duplicate read exclusion
  • read mapping quality score filter
  • read passing quality controls
  • being part of primary alignment
ADD COMMENTlink written 19 months ago by Noushin N560
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