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?