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For exome-sequencing, I was wondering how I should decide the "-mode" parameter? should I use "SNP" or "Indel" or both? I want to get both information in the final results, should I use "BOTH" -mode?
Use of the BOTH mode is no longer recommended, so please don't use that.
You should recalibrate the two types of variants separately. The recommended workflow (described in the VQSR tutorial here) is to first recalibrate for one type of variant (eg the snps, using -mode SNP), then recalibrate the resulting VCF file for the other type (eg the indels, using -mode INDEL). When you recalibrate for one type, the variants of the other type are emitted to the output file without modification. This way you don't have to separate them into different files before recalibration.
Geraldine Van der Auwera, PhD
Thanks Geraldine. Can i use the vcf file from haplotypecaller to do snp and indel recalibration separately? Or you recommend recalibration in a sequential one-after-another order?
We recommend the sequential-order workflow because it is the most efficient, but you can modify the workflow to suit your needs, sure.