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Bug #13469

closed

vcfbed2homref misreported homref region

Added by Abram Connelly almost 6 years ago. Updated almost 6 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
-
Target version:
-
Story points:
-

Description

When testing with the GIAB dataset, vcfbed2homref (v0.1.0) run on HG004 reported an end bound in a homozygous reference region that was before the start of following line.

The offending VCF line was:

7       85067121        rs149973664     TATTGCACAACAAAAGAAAAACAAAAGATATTTAGTAC  T       50      PASS    platforms=3;platformnames=CG,Illumina,10X;datasets=5;datasetnames=CGnormal,HiSeqPE300x,HiSeq250x250,10XChromium,HiSeqMatePair;callsets=8;callsetnames=CGnormal,HiSeqPE300xfreebayes,HiSeq250x250freebayes,HiSeqPE300xGATK,HiSeq250x250GATK,10XGATKhaplo,HiSeqMatePairfreebayes,HiSeqMatePairGATK;datasetsmissingcall=IonExome;callable=CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable,CS_HiSeq250x250freebayes_callable;filt=CS_CGnormal_filt,CS_HiSeqMatePairGATK_filt    GT:PS:DP:ADALL:AD:GQ    0/1:.:836:220,154:0,0:1460

With the corresponding BED file region being:

7       85058314        85067126
7       85067151        85068558
7       85068659        85071179
7       85071280        85073955

I believe the issue is that the bed file position wasn't updated when the homozygous start window was updated (around here).

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