How to deal with conflicting INFO field names in SnpSift?

Question

[bdolin]

I'm somewhat new to SnpSift, looking to annotate a VCF file with gnomAD population frequencies.

My VCF file has an existing INFO.AF field

##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

and gnomAD VCF also defines an INFO.AF field (with a different meaning)

##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate allele frequency in samples">

It looks like SnpSift's default behavior is to override an existing INFO.AF where there is a match to gnomAD - leaving me with a mix of INFO.AF fields.

Do I need to remove the existing INFO.AF field first, or is there a way, for instance, to rename the gnomAD annotation as I pull it in?

This is the command I'm running:

java -jar SnpSift.jar annotate gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz -info "AF" myVCF.vcf > myAnnotatedVCF.vcf

Thanks

[Pierre Lindenbaum]

and gnomAD VCF also defines an INFO.AF field (with a different meaning)

from my point of view, they do have the very same meaning

[Pierre Lindenbaum]

https://samtools.github.io/hts-specs/VCFv4.2.pdf

. Arbitrary keys are permitted, although the following sub-fields are reserved (albeit optional):

AF : allele frequency for each ALT allele in the same order as listed

[bdolin]

Unfortunately not. In one case, AF is the sample read frequency for the allele, and in the gnomAD case, AF is the population frequency for the allele.

[bdolin]

I see what you are saying - both have a same definition. But here's the actual output. This record was NOT found in gnomAD, and so the original INFO.AF is retained, as the sample read frequency:

chr1    187485  rs1423991279    G   A   242.77  PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.67;DB;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=-1.230e+00;QD=11.56;ReadPosRankSum=0.284;SOR=1.112;VQSLOD=2.47;culprit=FS GT:AD:DP:GQ:PL  0/1:9,12:21:99:271,0,175

Whereas this record WAS found in gnomAD, so INFO.AF was revised by SnpSift, but in this case is the population frequency:

chr1    942451  rs6672356   T   C   182.84  PASS    AC=2;AN=2;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=30.47;SOR=1.329;VQSLOD=1.87;culprit=DP;AF=9.99870e-01 GT:AD:DP:GQ:PL  1/1:0,6:6:18:211,18,0

[Pierre Lindenbaum]

Ah I see ! SnpSift is doing a little wrong here. You could use bcftools annotate --rename-annot to rename the field AF before/after snpSift:

    AF->old_AF
   (snpsift)
    AF->gnomad_AF
    old_AF->AF

[bdolin]

Thank you!