WARN VariantContextConverter:924 - Ran into Array Out of Bounds when accessing indices 0,1,2 of genotype .

[rezacsedu]

Hi there,

I'm trying to extract genomics data from VCF files. However, I'm experiencing the following warning.

2018-08-01 16:31:25 WARN VariantContextConverter:924 - Ran into Array Out of Bounds when accessing indices 0,1,2 of genotype [NA21126 A* GQ 99 PL 0,677 {CN=1, CNL=-1000,0,-67.74, CNP=-1000,0,-70.53, CNQ=99, GP=0,-70.53}].

I'm seeing 1000s of warnings like this. Is it a big issue or will it return fewer quality features? Please note that I'm using the following software versions:

Apache Spark: v2.3.0,
H2O: v3.14.0.1
Sparkling Water: v1.2.5
ADAM: v0.22.0
Scala: 2.11.8

[heuermh]

Generally, you may tweak validation for flat file formats using ValidationStringency

val genotypes = sc.loadGenotypes("sample0.vcf", stringency = ValidationStringency.SILENT)

As to that specific warning, the line number on the 0.22.0 release branch doesn't look like what I would expect, perhaps you might be on a different version?

In any case, if you could extract a short bit of VCF that demonstrates the warning, we could investigate further.

[rezacsedu]

@heuermh sorry for the wrong versions but here are the exact versions I'm using:

	<properties>
		<spark.version>2.2.1</spark.version>
		<scala.version>2.11.12</scala.version>
		<h2o.version>3.16.0.2</h2o.version>
		<sparklingwater.version>2.2.6</sparklingwater.version>
		<adam.version>0.23.0</adam.version>
	</properties>

[heuermh]

Yep, this line looks better https://github.com/bigdatagenomics/adam/blob/maint_spark2_2.11-0.23.0/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala#L924

It appears your data might have the wrong cardinality for the PL Number=G VCF FORMAT field
https://github.com/samtools/hts-specs/blob/master/VCFv4.3.tex#L399

Or perhaps we're doing something wrong. 😄

[rezacsedu]

Actually, I'm using the genetic variants data from the 1000 Genomes Project. However, when I use the following old versions, I don't experience such warnings:

    <properties>
        <spark.version>1.2.0</spark.version>
        <h2o.version>3.0.0.8</h2o.version>
        <sparklingwater.version>1.2.5</sparklingwater.version>
        <adam.version>0.16.0</adam.version>
</properties>

[heuermh]

I'm using the genetic variants data from the 1000 Genomes Project

That doesn't mean they're adhering correctly to the VCF specification. ;)

Which 1000G file(s) are you looking at, specifically?

when I use the following old versions, I don't experience such warnings

There have been 868 commits since version 0.16.0; I'd recommend trying newer versions rather than older ones.

[heuermh]

Closing due to lack of context for the error. Please reopen if you can provide an example 1000G file that causes the issue.