Hi,

I am trying to convert my vcf files to bgen using qctool https://www.well.ox.ac.uk/~gav/qctool_v2/documentation/examples/converting.html. This works for all but 6 chromosomes.

This error occurs, with a different line in each.

This is an example from chr 05:

!! Error (genfile::MalformedInputError): Source "file-path/data_chrxx.vcf.gz" is malformed on line 5145934..

When I visually look at the files they look fine?

Here is the header (I have X'd out number):

5       163915159       rs536200292     T       C       .       PASS    RefPanelAF=X.XXXXXX;AN=XXXXXX;AC=0;INFO=X.XXXXX       GT:ADS:DS:GP    

Any ideas what it could be?

Thanks!