BQSR Bootstrap: Combine hard-filtered SNP and Indel VCFs?


I'm trying to run BQSR on mouse WES tumor-normal data according to [1-6]. I'm on the first round of bootstrapping a knownSites.vcf to use for BQSR. I have just separated raw SNP and Indel variants from the rawVariants.vcf produced by HaplotypeCaller and hard filtered both into knownSNPSites1.vcf and knownIndelSites1.vcf according to [6]. My question is this: do I run BaseRecalibrator with just one of the knownSites.vcf files (SNP or Indel)? Do I combine them? Do I run BaseRecalibrator and just use two instances of --known-sites="/path/knownSNPSites1.vcf" --known-sites="/path/knownIndelSites1.vcf"?

I tried searching but couldn't find an exact answer. Thanks in advance.

[1] Data pre-processing for variant discovery. Available at:
[2] (howto) Recalibrate base quality scores = run BQSR. Available at:
[3] BaseRecalibrator. Retrieved from
[4] Base Quality Score Recalibration (BQSR). Retrieved from
[5] Confused about Bootstrapping a set of known sites for Base Recalibration. Retrieved from
[6] (howto) Apply hard filters to a call set. Retrieved from

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