The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?