Hello fellow Biostars,
I am currently working on an imputation from 6k to 50k data and one of the programmes in use is Beagle 4.0 (since I want to integrate pedigree data). When I performed a test run on a single chromosome, the following warning came up for 456 out of 986 SNPs:
"Skipping VCF record with no data" ---> Do you have any idea how this can happen?
I checked the manual/ documentation and other platforms and couldn't find any other comparable reports. Interestingly, the imputation was performed nevertheless and the accuracy seems to be very good as well. Still, I would like to get to the bottom of this problem/ warning.
All help and ideas are heartily appreciated!