Select SNP and reference monomorphic sites from a large callset
Recently, I have called genotype using
--includeNonVariantSites. I want to pull out the sites with one allele or
. in ALT column. I found the following command will also report the sites with
* or more than one allele listed in ALT column. I also tried to add
--restrictAllelesTo BIALLELIC, but the non-variant sites (sites with
. listed in ALT column) will be excluded. I do not know how to set these parameters to meet my requirements.
-T SelectVariants \ --selectTypeToInclude NO_VARIATION \ --selectTypeToInclude SNP \
Hope for your help.