Hello everyone,

I am trying to get genotype likelihoods using bcftools. I am using bcftools version 1.11, running bcftools mpileup and bcftools call. This is what I run:

bcftools mpileup -d 8000  -Ou -f $reference $input | bcftools call -mv -Ob -o $variants

However, when I check the columns INFO and FORMAT, I can't see the parameter genotype (GL) likelihood anywhere.

This is an example of my output:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  BOR_059_Tmontana
uce-2_consensus 708 .   T   C   137 PASS    DP=7;VDB=0.122391;SGB=-0.636426;MQ0F=0;AC=2;AN=2;DP4=0,0,0,7;MQ=60  GT:PL   1/1:167,21,0

As you can see, there are many other parameters but no GL. Another thing would be what can I do to put certain parameters, such as DP or MQ, in the FORMAT column directly (instead of those being the INFO column) when running bcftools mpileup?

All of these is because I want to filter my variants using an R package that was described last year. This package is called SNPfiltR and it seems really useful to explore the data and decide which thresholds to use when filtering.

Any help or tips would be appreciated. Thank you in advance!