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grenaud / glactools

command-line tools for the management of genotype likelihoods and allele counts
http://grenaud.github.io/glactools/
GNU General Public License v3.0
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--onlyGT confusion #28

Closed DcornishUCL closed 2 years ago

DcornishUCL commented 2 years ago

Hi,

I am converting a multi-sample VCF file to glactools acf format and I am using the --onlyGT flag since my VCF contains only genotypes. Weirdly, when I remove this flag, glactools still runs and outputs a file even though I have checked and confirmed there are no PL fields in my VCF...

grep "##FORMAT=" ALLchr_CEUlist_concat.vcf

FORMAT=

Does glactools interpret that a VCF contains only genotypes without the need for --onlyGT or am I misunderstanding the flag? Based on the comment in Vcf2ACF.cpp I assumed that glactools uses the PL field which is not present in my VCF.

Best,

Dean

grenaud commented 2 years ago

you do not use --onlyGT, it will use the PL fields, if they are missing, it will treat the site/sample as missing data.

Also, I encourage you to post on biostars and email me, others might have this question. Also, this does not seem like a bug :-)