I have produced a VCF from the best practice pipe line ( bams to gvcf's, genomicDBImport, GenotypeGVCFs, GatherVcfs). I'm using the version gatk-126.96.36.199.
I was wondering if I am using the command --exclude-non-variants correctly, my command is the following:
gatk SelectVariants \
-R /home/genomic_refseq.fna \
-V /home/WGS_RAW.vcf \
--select-type-to-include SNP \
--exclude-non-variants true \
I have produced files with and without the command and I get the same number of SNPs and with the command the file still contains non variant / monomorphic sites in the resulting VCF file.
Am I doing this correctly? Or do I need to perform this command separately? I would like to attain SNPs only at variant sites.
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