Make info tag separate column VCF

Question

[timothy.delory]

I am running ANGSD to get theta values for a VCF (I need to use a software that can account for small sample size/lower coverage). I have a PL (which I understand to be the same as GL) tag in my info field and PL (via GATK) values for my SNPS. However, when I run ANGSD I get the message

BAD SITE scaffoldx:y. return code:-2 while fetching GL tag rec->rid:3

giving me the impression it is not accessing my PL values. I changed my PL tags to GL, in my vcf and the error persisted. The output from ANGSD also states:

will use chrom, pos PL columns

This gave me the impression that maybe I need to make PL as a separate field rather than keeping it as one of my INFO tags. Is there a way to change a PL INFO tag to a separate field?

Thanks

[Ram]

Please include the angsd command that you're using. You may want to email the authors of ANGSD with a link to this post so they can help you - it is not a popular software on the forum.

[timothy.delory]

The command I used was

/angsd -vcf-gl angsd_x.vcf -doMajorMinor 1 -domaf 1