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How can I get UnifiedGenotyper to work on triploids
I am using the Gatk v3.1 UnifiedGenotyper for variant calling of some GBS type data in the plant genus Boechera. I have diploids as well as triploids, where I have the ploidy from a prior microsat run. The diploids work out well (I get some 150k variable loci), but I can't seem to get variants for the triploids.
Here's my initial call for the triploids:
Program Args: -T UnifiedGenotyper -R /home/A01768064/assembly/Bstricta_278_v1.fa -I mytripbam.list -o boechera_triploids.vcf -nt 22 -glm SNP -hets 0.001 -mbq 20 -ploidy 3 -pnrm EXACT_GENERAL_PLOIDY -stand_call_conf 50 -maxAltAlleles 2
I was able to call the triploids with the diploid option, but - obviously - this is not what I want.
I additionally ran the following relaxed stringency options.
hets 0.1 mbq 10
None of them return any variants.
The read group for one example file:
@RG ID:CR1308 LB:CR1308 SM:CR1308 PL:ILLUMINA
(with unique values for each sample; note that in the output vcf, the samples are appearing in the header line)
Additionally, I attached the slurm log file for the last mentioned run.
I am at a complete loss, what am I missing here?