As recommended in the GATK best practices the Variant Quality Score Recalibration has to be done separately for SNPs and Indels. But, I didn't find the way to do this split in a clean way (for instance vcftools). Does anybody know a tool to do this?
I already found a script that does the trick but I am surprised that this functionality is not included in the usual tools for processing VCF files.
The script in case it helps: http://ngsda.blogspot.com.es/2011/06/awk-script-to-seperate-snp-and-indel.html