Homozygous reference genotype for a GIAB genome
0
0
Entering edit mode
9 months ago
New2R ▴ 60

GIAB VCFs (v4.2.1) provides 0/1, 1/0 (ALT-heterozygous) & 1/1 (ALT- homozygous) genotypes (in addition 1/2, 2/1, & 2/2 where there are more than one ALT alleles). GIAB also provides a BED file where any other position not in the VCF can be consider high confidence homozygous reference.

I have a list of SNP rs IDs for which I need to extract the homozygous reference genotype, say for NA12878. Is there a simple why to achieve this?

The primary purpose is to allow genotype concordance measurement with a microarray platform, measure recall and precision.

GIAB IDs reference rs Homozygous • 338 views
ADD COMMENT

Login before adding your answer.

Traffic: 2144 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