Effect of dbSNP build differences in variant calling
0
0
Entering edit mode
2.4 years ago

I want to call variants on prealigned CRAM files for a 1000genomes sample, available for download. However, the dbSNP build used to recalibrate base quality scores (the dataset is already recalibrated) for all 1000genomes phase 3 pipelines is dbSNP build 142 which is the 2014 version (current build is 151)

Should I nevertheless proceed with calling variants despite the build differences ? Would you recommend re-recalibrating the CRAM (after conversion to BAM) with the latest dbSNP build ?

assembly dbSNP GATK GRCh38 variantcalling • 612 views
ADD COMMENT

Login before adding your answer.

Traffic: 2114 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