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Exclude mono morphic variants from VCF file

Hello Everyone

I am trying to exclude all the mono-morphic variants from GWAS vcf file. I used GATK SelecttVaraint walker with -env option.

Not sure am i doing the right thing or there in another way to exclude them?

Regards Moeen

snp
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updated by GouthamAtla GouthamAtla • written by malik.moin • malik.moin

Do you mean to say if alt column has a . ?

awk '{ if ( $0~/^#/ ) { print } else if ( $5!="." ) { print } }' in.vcf > out.vcf
• 1 views • link
written by GouthamAtla GouthamAtla

Thanks ...

i want to exclude non-variant sites.. which could be '.' or same alternate allele .

• 1 views • link
written by malik.moin • malik.moin

1 answer 

vcf-subset --exclude-ref in.vcf > out.vcf
• 1 views • link
written by GouthamAtla GouthamAtla

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