The current GATK version is 3.3-0

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

# Can I use GATK on non-diploid organisms?

Posts: 71GATK Developer mod
edited October 24 in FAQs

In general most GATK tools don't care about ploidy. The major exception is, of course, at the variant calling step: the variant callers need to know what ploidy is assumed for a given sample in order to perform the appropriate calculations.

### Ploidy-related functionalities

As of version 3.3, the HaplotypeCaller and GenotypeGVCFs are able to deal with non-diploid organisms (whether haploid or exotically polyploid). In the case of HaplotypeCaller, you need to specify the ploidy of your non-diploid sample with the -ploidy argument. HC can only deal with one ploidy at a time, so if you want to process different chromosomes with different ploidies (e.g. to call X and Y in males) you need to run them separately. On the bright side, you can combine the resulting files afterward. In particular, if you’re running the -ERC GVCF workflow, you’ll find that both CombineGVCFs and GenotypeGVCFs are able to handle mixed ploidies (between locations and between samples). Both tools are able to correctly work out the ploidy of any given sample at a given site based on the composition of the GT field, so they don’t require you to specify the -ploidy argument.

For earlier versions (all the way to 2.0) the fallback option is UnifiedGenotyper, which also accepts the -ploidy argument.

### Cases where ploidy needs to be specified

1. Native variant calling in haploid or polyploid organisms.
2. Pooled calling where many pooled organisms share a single barcode and hence are treated as a single "sample".
3. Pooled validation/genotyping at known sites.

For normal organism ploidy, you just set the -ploidy argument to the desired number of chromosomes per organism. In the case of pooled sequencing experiments, this argument should be set to the number of chromosomes per barcoded sample, i.e. (Ploidy per individual) * (Individuals in pool).

## Important limitations

Several variant annotations are not appropriate for use with non-diploid cases. In particular, InbreedingCoeff will not be annotated on non-diploid calls. Annotations that do work and are supported in non-diploid use cases are the following: QUAL, QD, SB, FS, AC, AF, and Genotype annotations such as PL, AD, GT, etc.

You should also be aware of the fundamental accuracy limitations of high ploidy calling. Calling low-frequency variants in a pool or in an organism with high ploidy is hard because these rare variants become almost indistinguishable from sequencing errors.

Post edited by Geraldine_VdAuwera on
Tagged:

• Posts: 1Member

As GATK2 can handle Mitochondrial DNA, is there a recommended ploidy setting for human Mitochondria? I understand that mtDNA can vary dramatically in how many copies are present in a cell, but is there some sort of consensus value? (e.g. some sort of function of mean coverage)

Thank-you very much!

• Posts: 71GATK Developer mod

We've experimented with 50 to 100 but we make no optimality claims on that - probably a better number would be the ratio of (mean coverage in the MT contig) / (mean coverage in somatic chromosomes)

• Posts: 3Member

@delangel are there any other recommended settings for MT with GATK?

• Posts: 3Member
edited September 2012

@delangel How does UG use this ploidy information for calling variants in MT? For SNPs at any position we dont expect more than 4 alleles (ATGC). In our low-pass data we have 5-7X coverage overall, and ~700X in case of mitochondria.

Post edited by sahiilseth on
• Posts: 71GATK Developer mod

It's internal machinery needs to know the organism ploidy (i.e. number of chromosomes inside) to work well (btw number of possible different alleles is different than ploidy). Given your coverage I'd start with -ploidy 100 or so