Closed isinaltinkaya closed 9 months ago
Thank you for the test case.
The program call
expects direct output from mpileup
and unaware of GL, trims only PL fields when alleles are removed. In principle it could be made smarter, but I am not convinced it is worth it. Simply change the pipeline to
mpileup | call | tag2tag
Hi,
I am using version: 1.18-31-g4014f7e2 (using htslib 1.18-72-g9e1ffd85).
Commands:
I get this error:
It works fine when I remove the bcftools plugin tag2tag part and directly pipe to bcftools call.
Input files: