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resource datasets for VQSR
I am working on Arabidopsis and there are published high-quality snp_indel data for this species. I got the vcf file named "1001genomes_snp-short-indel_only_ACGTN.vcf". I used this as known-sites for the BQSR step, and should I also use this as resource for VQSR? Is It required to recalibrate snp (
-mode SNP) and indel (
-mode INDEL) separately? As the resource includes both snp and indel, is it reasonable to do VQSR in one run?
Thanks a lot for your time.