GenotypeGVCFs emitting spanned allele without the spanning variant

[tfenne]

Bug Report

We're finding that in rare instances that GenotypeGVCFs can emit a variant with a spanned allele (*), and a genotype that references the spanned allele, but fail to emit the upstream spanning variant. This seems like a bug to me - either the spanning variant should be emitted or the spanned allele should revert to a reference call.

FWIW I have a sneaking suspicion that this is related to setting a non-zero value for -stand-call-conf (see #5793). My guess is that in one part of the code it determines the upstream variant will be emitted so retains the allele as spanned, but then somewhere later the upstream variant is filtered out.

Affected tool(s) or class(es)

GenotypeGVCFs

Affected version(s)

• Latest public release version [4.1.2.0]
• Latest master branch as of [not tested]

Description

Here's the example from the VCF in the attached zip file:

#CHROM  POS       ID  REF            ALT      QUAL     FILTER  INFO  FORMAT                    test_sample
chr17   46806234  .   TC             T        148.64   .       ...   GT:AD:DP:F1R2:F2R1:GQ:PL  0/1:208,25:239:116,16:90,8:99:156,0,6824
chr17   46806237  .   TTCTCTCTCTCTC  TTCTC,*  1528.04  .       ...   GT:AD:DP:F1R2:F2R1:GQ:PL  1/2:3,60,33:174:1,29,20:1,21,11:99:3633,1088,2142,1538,0,3285

You can see from this that a) the first variant does not have a spanned allele, implying that there cannot be a spanning event further upstream and b) the second variant has a spanned allele that is present in the 1/2 genotype.

Steps to reproduce

The attached zip file contains a reduced test case with a 3-record gVCF and a 2-record VCF that exhibits the problem. To reproduce:

1. Unzip the attached zip file
2. Edit command.sh to put in the path to HG19
3. Run . command.sh in the directory with the extracted files

Expected behavior

Either the spanning variant should be emitted, or the spanned allele should not be.

Actual behavior

A spanned allele is emitted when there is no spanning variant!

ZIP file with test case: spanned_allele_not_spanned.zip

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