Question: plink file convert to vcf & comparison other WGS vcf file
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gravatar for phswin92
8 weeks ago by
phswin920
phswin920 wrote:

Hello

I have a file converted from plink to vcf then I want to compare this vcf and other WGS vcf file.

but converted from plink to vcf file format doesn't run wgs vcf comparison tools.

CHROM POS  ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 sample5 sample6   
1       761252  AX-37361829     C       T       .       .       PR      GT      0/0     0/0     0/0     0/0     0/0     0/0        
1       762485  AX-83277131     C       A       .       .       PR      GT      0/1     0/0     0/0     0/0     0/0     0/0        
1       762589  AX-113622880    C       G       .       .       PR      GT      0/1     0/0     0/0     0/0     0/0     0/0

can I merge sample1~7 GT to run the comparison tool??

I want to run vcf-compare or hap.py , but that vcf format doesn't run

please help

sequencing • 117 views
ADD COMMENTlink modified 13 days ago by Biostar ♦♦ 20 • written 8 weeks ago by phswin920
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