Filter criteria for variants based on GBS data
Are there recommended filter criteria for variants based on GBS data?
I currently use this filter formula that is used in bcbio for WGS based variants soft-filtering
bcftools --soft-filter GATKCutoffSNP -e TYPE="snp" && (MQRankSum < -12.5 || ReadPosRankSum < -8.0 || QD < 2.0 || FS > 60.0 || MQ < 30.0) -m + input.vcf.gz.
Not sure if all filter criteria in this formula make sense for GBS data.
And some other new additional filter criteria might make sense for GBS. For example based on:
- Read Depth
- Allele Number
- Alternative allele count
- Expected target GBS regions based on in sillicio reference genome digestion
- other values ?
Does anyone know of recommended GBS filter criteria/formula?
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Here in this article, I have covered some of the filtering criteria for variant filtering from the GBS data. I hope it will be helpful to you.