Hi,
when I run HaplotypeCaller on on a bunch of .g.vcf files, at the joint discovery stage, it creates the output vcf with the header, but doesn't output the variants.
There are a couple of warnings I don't quite get. Any idea?
Attached files are (1) the log from GenotypeGVCFs, (2) the first 200 lines from one of the .g.vcf files, and (3) the full vcf created by the joint genotyping.
Thanks,
Steph
NB: added a .txt extension as uploading a .vcf doesn't work