--max-alleles argument not recognized
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6.3 years ago
boris • 0

It seems as if I can't get --max-alleles to be recognized no matter what I do.  The command below gets interpreted as requesting snps with at most 2 alleles.  Any suggestions?  What am I doing wrong?

vcftools --gzvcf combined.vcf.gz --maf 0.05 --max-alleles 3 --max-maf 0.5 --hwe 1e-8 --minQ 40 --012 --max-missing 0.95 --chr chr22 --out combined.chr22.common

VCFtools - v0.1.13

(C) Adam Auton and Anthony Marcketta 2009

 

Parameters as interpreted:

        --gzvcf combined.vcf.gz

        --chr chr22

        --maf 0.05

        --max-alleles 2

        --max-maf 0.5

        --hwe 1e-08

        --minQ 40

        --max-missing 0.95

        --012

        --out combined.chr22.common

 

SNP vcftools • 1.6k views
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