More Information in INFO field of final VCF file

[faramarzgsm]

Developer team
thanks for your support.
by running this command:

docker run
-v "$OUTDIR":/output
-v "$REF_DIR":/ref
google/deepvariant:1.9.0
/opt/deepvariant/bin/run_deepvariant
--model_type=WES
--ref="/ref/$(basename "$REFERENCE")"
--reads="/output/${SAMPLE}.dedup.bam"
--output_vcf="/output/${SAMPLE}.deepvariant.vcf.gz"
--output_gvcf="/output/${SAMPLE}.deepvariant.g.vcf.gz"
--vcf_stats_report
--num_shards=$THREADS \

I see just information such as GT:GQ:DP:AD:VAF:PL in the FORMAT field.

How to run DeepVariant to add more information in the FORMAT or INFO field in the final VCF file such as blew:
AD, ADF, ADR, AF, BQ, DP, MQ, SB or more...
these information are critical for post process quality check and filtering variants which could be present in VCF v4.3.

[kishwarshafin]

@faramarzgsm these are optional fields that require code changes to add them to the VCF file. Usually GT:GQ:DP:AD:VAF:PL contains sufficient information for filtering. What are the types of information are you looking to incorporate?

[faramarzgsm]

I'm looking for these critical QC informations:

RDF: Reference allele Depth in Forward reads
RDR: Reference allele Depth in Reverse reads
ADF: Alternative allele Depth in Forward reads
ADR: Alternative allele Depth in Reverse reads
MQ: Map Quality
QD: Quality by Depth = QUAL / DP

[kishwarshafin]

@faramarzgsm ,

Reporting these in the VCF would require us to carry these information from make_examples to postprocess_variants which will add quiet a bit of complexity in code. One of the way to QC DeepVariant is the GQ value which is phred score of the confidence on the call. In our publications, we have shown that the GQ values are very well calibrated to the truth (meaning at GQ20, the confidence is 99% and you should only expect 1 out of 100 errors at GQ20). I would strongly suggest using GQ as a filter if you are optimizing for accuracy as it would be most accurate than coming up with heuristic measures with these values.

[kishwarshafin]

hi @faramarzgsm I am going to close this issue, if you need further clarification, please feel free to reopen.