Question: what does ./1 in a VCF file means
0
gravatar for raalsuwaidi
8 weeks ago by
raalsuwaidi0 wrote:

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

snp sequence genome vcf • 118 views
ADD COMMENTlink modified 8 weeks ago by bruce.moran790 • written 8 weeks ago by raalsuwaidi0
1

i have a vcf file provided by my professor

ask your professor ?

ADD REPLYlink written 8 weeks ago by Pierre Lindenbaum128k

I wanted to avoid too many questions to him

ADD REPLYlink written 8 weeks ago by raalsuwaidi0
2
gravatar for bruce.moran
8 weeks ago by
bruce.moran790
Ireland
bruce.moran790 wrote:

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

ADD COMMENTlink written 8 weeks ago by bruce.moran790

Thank you so much it makes sense for me now

ADD REPLYlink written 8 weeks ago by raalsuwaidi0
2

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

ADD REPLYlink written 8 weeks ago by genomax83k
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