what does ./1 in a VCF file means
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3.7 years ago
raalsuwaidi ▴ 100

Hi all, i am new to the genome area. i am trying with impute2 and i have a vcf file provided by my professor. i am trying to run the perl script coming with impute2 to generate the get file but i am receiving an error ERROR: Genotype |./1| (i=76) at site 16256767 is not in accepted format. i know that 0/1 means its un phased, but i dont know what ./1 means. as i mentioned the goal is to generate the gen file for impute2

vcf genome snp sequence • 980 views
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i have a vcf file provided by my professor

ask your professor ?

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I wanted to avoid too many questions to him

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3.7 years ago
bruce.moran ▴ 960

Have a look at the VCF format specs, page 5/6 about genotype/GT field.

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Thank you so much it makes sense for me now

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