Import multiple .vcf.bgz by chromosome fails on chr Y

Hail Query & hailctl
1

I’m trying to import the 1000 genomes project data using the files found here but when i include the Y chromosome into my paths list I get the following error.

Hail version: 0.2.81-edeb70bc789c
Error summary: HailException: invalid sample IDs: expected same number of samples for all inputs.
 file:/Users/tony/Projects/nat-variation/data/interim/block_zipped_IGSR/ALL.chr7.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.vcf.bgz has 2504 ids and
 file:/Users/tony/Projects/nat-variation/data/interim/block_zipped_IGSR/ALL.chrY.phase3_integrated_v2b.20130502.genotypes.vcf.bgz has 1233 ids.

What is the best way to handle this discrepancy?

Is there a way to include the Y chromosome using hail as it is or would it be best to impute empty instances into the .vcf.bgz file for the missing ids?

2

This is an uncommon representation – typically we’ve seen loci on the Y chromosome include individuals of with sex karyotypes, and those without a Y chromosome have uncalled genotypes on that chromosome.

This appears to be an imputed genotype data release from 1kg, which we’re not familiar with (we’re familiar with the whole genome sequenced VCFs).

3

aaaah I see, is there a way to impute uncalled genotypes in the Y chromosome from hail?