error in vcfeval with GT

[Alexandra Vatsiou]

Hello, 

I am running vcfeval for Platinum Genome samples as follows: 

rtg vcfeval -c vcf.gz -b NA12877.vcf.gz --no-gzip --decompose -t hg38_alt_aware/ -o test --sample NA12877,S1 --vcf-score-field QUAL --bed-regions ConfidentRegions.bed.gz

And I have the following error: 

```

2023-02-01 19:18:26 Variant orientors per pass: [unphased (2 haplotypes):unphased (2 haplotypes)] 2023-02-01 19:18:27 Got an exception processing calls VCF record: chr1 2363769 . G AAAAAA 0.00 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=55;FS=0.000;MQ=216.91;QD=9.86;SOR=2.786;FractionInformativeReads=0.855 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/2:0,26,21:0.553,0.447:47:0,13,9:0,13,12:49:598,520,77,664,0,78:4.5000e+02,4.5000e+02,5.1882e+01,4.5000e+02,4.9960e-05,5.3000e+01:0.00,28.00,31.00,28.00,56.00,31.00:0,0,38,9:0,0,23,24 com.rtg.vcf.S: VCF record GT contains allele ID out of range, record: chr1 2363769 . G AAAAAA 0.00 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=55;FS=0.000;MQ=216.91;QD=9.86;SOR=2.786;FractionInformativeReads=0.855 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/2:0,26,21:0.553,0.447:47:0,13,9:0,13,12:49:598,520,77,664,0,78:4.5000e+02,4.5000e+02,5.1882e+01,4.5000e+02,4.9960e-05,5.3000e+01:0.00,28.00,31.00,28.00,56.00,31.00:0,0,38,9:0,0,23,24 at com.rtg.vcf.eval.ap.a(VariantFactory.java:168) at com.rtg.vcf.eval.ap$b.a(VariantFactory.java:133) at com.rtg.vcf.eval.ap$b.b(VariantFactory.java:96) at com.rtg.vcf.eval.av.a(VcfRecordTabixCallable.java:121) at com.rtg.vcf.eval.av.call(VcfRecordTabixCallable.java:56) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 2023-02-01 19:18:32 Error: VCF record GT contains allele ID out of range, record: chr1 2363769 . G AAAAAA 0.00 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=55;FS=0.000;MQ=216.91;QD=9.86;SOR=2.786;FractionInformativeReads=0.855 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/2:0,26,21:0.553,0.447:47:0,13,9:0,13,12:49:598,520,77,664,0,78:4.5000e+02,4.5000e+02,5.1882e+01,4.5000e+02,4.9960e-05,5.3000e+01:0.00,28.00,31.00,28.00,56.00,31.00:0,0,38,9:0,0,23,24 2023-02-01 19:18:32 Run failed in 10 s.

```

This is how it looks in the vcf the variant

```

bcftools view .vcf.gz -r chr1:2363769 -H chr1 2363769 . G AAAAAA 0 PASS AC=1,1;AF=0.5,0.5;AN=2;DP=55;FS=0;MQ=216.91;QD=9.86;SOR=2.786;FractionInformativeReads=0.855 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/2:0,26,21:0.553,0.447:47:0,13,9:0,13,12:49:598,520,77,664,0,78:450,450,51.882,450,4.996e-05,53:0,28,31,28,56,31:0,0,38,9:0,0,23,24 chr1 2363769 . G AAAA 0 PASS AC=1,1;AF=0.5,0.5;AN=2;DP=55;FS=0;MQ=216.91;QD=9.86;SOR=2.786;FractionInformativeReads=0.855 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/2:0,26,21:0.553,0.447:47:0,13,9:0,13,12:49:598,520,77,664,0,78:450,450,51.882,450,4.996e-05,53:0,28,31,28,56,31:0,0,38,9:0,0,23,24

Even if I remove those 2 variants, it keeps failing

```

2023-02-01 19:41:04 Got an exception processing calls VCF record: chr1 4813348 . CCG GACACACACCA 0.00 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=33;FS=0.000;MQ=246.86;QD=6.30;SOR=0.693;FractionInformativeReads=0.364 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/2:0,6,6:0.500,0.500:12:0,2,3:0,4,3:47:214,161,50,168,0,50:2.0785e+02,1.5785e+02,4.9890e+01,1.6541e+02,8.8013e-05,5.0000e+01:0.00,3.00,6.01,3.00,6.00,6.01:0,0,6,6:0,0,5,7 com.rtg.vcf.S: VCF record GT contains allele ID out of range, record: chr1 4813348 . CCG GACACACACCA 0.00 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=33;FS=0.000;MQ=246.86;QD=6.30;SOR=0.693;FractionInformativeReads=0.364 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/2:0,6,6:0.500,0.500:12:0,2,3:0,4,3:47:214,161,50,168,0,50:2.0785e+02,1.5785e+02,4.9890e+01,1.6541e+02,8.8013e-05,5.0000e+01:0.00,3.00,6.01,3.00,6.00,6.01:0,0,6,6:0,0,5,7 at com.rtg.vcf.eval.ap.a(VariantFactory.java:168) at com.rtg.vcf.eval.ap$b.a(VariantFactory.java:133) at com.rtg.vcf.eval.ap$b.b(VariantFactory.java:96) at com.rtg.vcf.eval.av.a(VcfRecordTabixCallable.java:121) at com.rtg.vcf.eval.av.call(VcfRecordTabixCallable.java:56) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 2023-02-01 19:41:07 Error: VCF record GT contains allele ID out of range, record: chr1 4813348 . CCG GACACACACCA 0.00 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=33;FS=0.000;MQ=246.86;QD=6.30;SOR=0.693;FractionInformativeReads=0.364 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/2:0,6,6:0.500,0.500:12:0,2,3:0,4,3:47:214,161,50,168,0,50:2.0785e+02,1.5785e+02,4.9890e+01,1.6541e+02,8.8013e-05,5.0000e+01:0.00,3.00,6.01,3.00,6.00,6.01:0,0,6,6:0,0,5,7 2023-02-01 19:41:07 Run failed in 9 s.

``` 

If I remove all records with GT=1/2, it works OK. 

Ideally it should work for those variants. Could you please help me understand why I have this error and how I can resolve it? 

Thank you in advance. 

Best,

Alexandra

[Alexandra Vatsiou]

I forgot to mention, I am using rtg-tools=3.12.1

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Alexandra Vatsiou
Bioinformatics Scientist at Illumina

http://www.linkedin.com/pub/alexandra-vatsiou/29/6a1/161

https://sites.google.com/site/alexvatsiou/

[Sean Irvine]

Hi Alexandra,

The VCF records in your example are invalid.

In particular, what allele would be associated with allele "2" as there is only 1 alternate allele ( AAAAAA) listed in the record?

I think you need to look earlier in your pipeline to discover where the invalid GT is coming from.

Sean.

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