Non-left-aligned variant in sparse_split_multi Error


I am trying to export only non-reference rows from the MT merging 5k gvcfs.
My pipeline is as below.

hl.len(densified_mt.alleles) > 1

But in the MT.write() function execution, I got an error at the very last minute.

Please let me know how to correct it or recommend another pipeline if you have.


Hi Hail team,

I am looking forward to your advice eagerly. If you need any more information, please let me know. Thank you always.


This is an unexpected input – Hail’s sparse matrix utilities work against left-aligned variants. What caller generated your GVCFs?

Hi @tpoterba,

Thank you for your response. We applied the same variant calling pipeline including Haplotypecaller (GATK) for all genomes. By the way, this error occurred not in the “hl.experimental.sparse_split_multi” step, but in the “MT.write” step. Why does it happen?

Please suggest possible solutions you think. Thank you.