Exclude non variant sites

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Victoria Buswell

• October 27, 2021 15:26

Hello,

I have produced a VCF from the best practice pipe line ( bams to gvcf's, genomicDBImport, GenotypeGVCFs, GatherVcfs). I'm using the version gatk-4.2.0.0. 

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 \
-O /home/WGS_RAW_SNPs.vcf

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. 

many thanks.

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• 

  Genevieve Brandt (she/her)

  • October 28, 2021 15:35

  Hi Victoria Buswell,

  Thanks for writing in with your question! Could you give some examples of the non variant sites that appear in your VCF after this command?

  Best,

  Genevieve

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