I'm running PINDEL (https://github.com/genome/pindel) and then i convert the output into .vcf with pindel2vcf (https://github.com/genome/pindel/blob/master/src/pindel2vcf.cpp). The problem is that when i head the .vcf file the genotype field "PL" or "Phred-scale" is present but absent when i tail it. So later in my pipeline, i want to use that VCF file generated by pindel2vcf as input into duphold (https://github.com/brentp/duphold), but when i start to running it says:
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
In don't know if this is a problem of duphold or pindel, or is just a non reported incompatibility. Any help would be great.
All the paths are correct. I tried with the -G (GATK compatibility) argument of pindel2vcf and without it but i got the same problem.