I work on Arabidopsis and now am running the BQSR. I have questions about the -knownSites option:
I have a population-level snp.vcf file which is quite large and I also have individual-level snp.vcf files. Should I use the population-level one or just choose one of the individuals? As the population-level snp file is quite large, I am worried it will slow down the process.
The indels and snps are included in a single file, should I separate them into independent files for the BQSR?