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Select SNP and reference monomorphic sites from a large callset

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


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