Question: Convert IMPUTE2 to VCF while keeping phase information
3
gravatar for lkmklsmn
3.6 years ago by
lkmklsmn890
United States
lkmklsmn890 wrote:

Hi,  

I have imputed genotypes using the IMPUTE2 software. Now I need to convert my IMPUTE2 formatted genotypes into VCF. I have used the qctool to do so. However, the resulting VCF file has lost the phasing information. Is there any tool that allows me to convert IMPUTE2 to VCF while keeping the phasing information?  

Thanks

conversion phasing impute2 vcf • 1.9k views
ADD COMMENTlink modified 9 weeks ago by croshong750 • written 3.6 years ago by lkmklsmn890
6
gravatar for lkmklsmn
3.5 years ago by
lkmklsmn890
United States
lkmklsmn890 wrote:

I ended up using shapeit (version v2.837) -convert function to convert IMPUTE2 to VCF while keeping phase information.

ADD COMMENTlink written 3.5 years ago by lkmklsmn890
0
gravatar for croshong75
9 weeks ago by
croshong750
croshong750 wrote:

Hi all

I tried to use shapeit to convert impute2 result to vcf file

with the following command

before doing that I changed the file extension *.impute2 ---> *.haps

with *.haps

./shapeit -convert --input-haps [ prefix of haps file ] --output-vcf [ prefix of haps file ].vcf

I got the following error

Reading sample list in [*.sample] * 807 individuals included

Reading site list and haplotypes in [*.haps]

ERROR: Line=1 found=2426 fields, expected=1619 or 1620

It seems that the file format requirement of shapeit is different from impute2 file format or there may be any other option

for conversion in shapeit.

How can I fix this problem? or is there any other tool to conversion impute2 result to vcf format while retaining phasing information?

Thanks

regards

ADD COMMENTlink written 9 weeks ago by croshong750

plink 2.0 supports this:

plink2 --haps <full .haps filename> --export vcf --out <output filename prefix>
ADD REPLYlink written 9 weeks ago by chrchang5235.3k
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