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
./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?