help with pindel2vcf

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4.8 years ago

tebb • 0

Hi everyone,

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.

Thank you,

B.

pindel pindel2vcf VCF duphold structural variant • 1.2k views

ADD COMMENT • link 4.8 years ago by tebb • 0

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That is a [common] warning message. Do you know if duphold requires the PL tag?

ADD REPLY • link 4.8 years ago by Kevin Blighe 87k

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