Filter criteria for variants based on GBS data
0
0
Entering edit mode
4 weeks ago
William ★ 4.9k

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?

gbs filter • 129 views
ADD COMMENT
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2384 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6