Dear all,
Recently, I have called genotype using GenotypeGVCFs
with --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.
Best
Zhuqing