vcftools 012 output missing homozygous minor genotype

0

It seems that my .012 file never has any 0 entries (homozygous minor) when run on a sample of over 300 vcf files.  I'm looking at common variants.  What am I doing wrong?
 

vcftools --gzvcf combined.vcf.gz --maf 0.05 --max-maf 0.5 --hwe 1e-8 --minQ 40 --012 --max-missing 0.95 --chr chr12 --out combined.chr12.common

VCFtools - v0.1.13

(C) Adam Auton and Anthony Marcketta 2009

 

Parameters as interpreted:

        --gzvcf combined.vcf.gz

        --chr chr12

        --maf 0.05

        --max-alleles 2

        --max-maf 0.5

        --hwe 1e-08

        --minQ 40

        --max-missing 0.95

        --012

        --out combined.chr12.common

 


SNP


vcftools

• 2.4k views

updated 2 hours ago by

0

written 6.1 years ago by

0



Source link