Understanding DPF from VCF file

[bio_informatics]

I have VCF file version:, ##fileformat=VCFv4.1 from isaac variant caller.

Header of the output:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HCC2218C

chrM 12941 . G A 3070.00 PASS SNVSB=-34268.1;SNVHPOL=4 GT:GQ:GQX: DP: DPF:AD 1/1:3070:3070:31471:2644:22,31437

If I read that, it means the depth coverage for this particular variant call is 2644.
Please correct, if I am wrong.

So, if the depth of coverage is high during variant calling, this particular SNP/variant is one of the higher disturbance causing? Is that correct? The higher DP, the high chances of a variation being causal.

[vivek_]

The depth at that locus appears to be 31,471 as suggested by DP & AD fields. It won't be clear what DPF means unless you post the full header.

[bio_informatics]

My apologies, I meant DP only.
Not DPF.
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping">

##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping">

While looking for variants, how much cut off DP be incorporated or set in order to look for the desired variants?

[vivek_]

That read depth appears very high compared to what you get from ordinary exome sequencing data but you'd also likely have to look at the allele depth for the alternate allele, which appears to be very high in this case, 22 reads suggesting reference allele vs 31,437 suggesting alternate allele. So the variant is likely true.

For usual exome sequencing studies anywhere > 10 reads with adequate support for the alternate allele from both strands and high mapping/base qualities is presumed to be good, since your depth is so high, you could may be plot the DP values for the whole dataset and create a customized cut off.

[bio_informatics]

By Allele Depth, it means here:
if ref is 'G' and alt is 'A' and AD is '22,31437' you got 22 G reads and 31437 A reads
Please correct me if I am wrong.