Genotyping samples at a predetermined list of locations
1
0
Entering edit mode
14 months ago

Tools like HaplotypeCaller look at a BAM file and locate places where it differs from the reference. Thats great for variant discovery, but not so great if you want to genotype a sample, because distinguish between being homozygous reference and not having sufficient data to call a variant. That is, its not safe to assume a sample is homozygous reference just because HaplotypeCaller doesn't call a SNP.

Is there an obvious way to provide a redetermined set of locations (say dbSNP) and return, say, the properly quality adjusted log-likelihood of each genotype at each location?

SNP GATK Variants Genotyping • 453 views
ADD COMMENT
0
Entering edit mode

Not sure if that fully solves your question, but Freebayes can take a VCF as input for force-calling of those positions.

ADD REPLY
0
Entering edit mode
14 months ago
bari.ballew ▴ 300

You can force-call over a set of alleles with HaplotypeCaller. Look at the flags --force-call-filtered-alleles and --alleles.

ADD COMMENT

Login before adding your answer.

Traffic: 2269 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