Hi, when I split multiallelic variants I get an error in one case: hail.utils.java.FatalError: HailException: RVD error! Keys found out of order: Current key: { locus: { contig: chr3, position: 16902883 }, alleles: [2; N, GGGGTGCGC] } Previous key: { locus: { contig: chr3, position: 16902883 },…

Hi! This error is almost always caused by splitting a dataset that already has some split alleles. Do you call split multi hts twice? Is your input dataset already split? Try filtering to the locus printed in the error message and verify your input dataset has exactly one row, not two.

Error split multiallelic

Hail Query & hailctl

danking Split this topic March 22, 2021, 4:32pm 3

2 posts were split to a new topic: When running split_multi_hts, I received a key out of order error. Why do I receive that and what should I do?

Topic		Replies	Views
RVD error! Keys found out of order Hail Query & hailctl	2	710	February 12, 2020
How "alleles" filed in a key generated Hail Query & hailctl	3	337	March 16, 2021
When running split_multi_hts, I received a key out of order error. Why do I receive that and what should I do? Hail Query & hailctl	5	480	June 13, 2022
Multiallelic Split Plink Error Hail Query & hailctl	0	368	August 11, 2023
VariantDatasetCombiner - dataset contains both multiallelic variants and duplicated loci for review Hail Query & hailctl	13	430	July 24, 2023

Error split multiallelic

Related Topics