Filter criteria for variants based on GBS data

Question

[William]

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?

[Renesh]

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.