NA causes export errors out

[iris-garden]

MCMC said:

I was trying to export a MatrixTable to Plink or VCF format. Both error out due to NA.

My export_plink code is:
hl.export_plink(mt, filePrefix+‘.HailQC’, ind_id = mt.s)

and it returns:
FatalError: HailException: unphased_diploid_gt_index only supports ploidy == 2. Found 0.

My export_vcf code is:
hl.export_vcf(mt, filePrefix+‘.HailQC.vcf’)

and it returns:
FatalError: HailException: VCF spec does not support phased haploid calls.

Both worked after I dropped variants that has NAs. My Hail version is 0.2.126-ee77707f4fab.

Please help. Thank you!

patrick-schultz said:

Hi MCMC, sorry you’re running into difficulty!

This isn’t about NAs. Your dataset has monoploid calls in it. export_vcf should be able to handle that, but there’s a bug which was fixed in this PR, which will be in the next release (which should be this week).

export_plink does not support monoploid calls. See the docs here for details.

MCMC said:

Hi patrick-schultz , thank you for your reply.

This is human variants called from WGS. Is it normal that it contains monoploid calls? Is it because of the sex chromosomes?

patrick-schultz said:

That’s most likely, yeah.

MCMC said:

Thank you!