Hi,

I used platypus to call variants from hg19 aligned reads. This worked perfectly fine. I did the alignment with hg38, platypus ran through but only created a vcf containing the header and header description.

The log file says: "DEBUG - There are 0 filtered variant candidates in reads which overlap the region" for all regions. Therefore, it's not surpirising that the vcf output does not contain any varinats.

I already tried different samples, different hg38 references but nothing seems to work. The alignment pipeline is exactly the same as in the first run with hg19 except different reference. What I am doing wrong?

Best,

Patrick.