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# CombineVariants: GT field is not updated when merging variants with different ALT alleles

Member
edited September 2013

HI

my two VCF files have different alternate allele at the same position as i have called the variants using two different callers. When i run combine Variants on the both my GT field is not updated properly. AD field is also not updated properly but i ran Variant Annotator and that fixes that issue.

VCF 1:

chr1    87708015    rs58006838  C   T   145.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=-1.479;DB;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=3.9299;MLEAC=1;MLEAF=0.500;MQ=68.54;MQ0=0;MQRankSum=-1.109;QD=10.41;ReadPosRankSum=0.925  GT:AD:DP:GQ:PL  0/1:3,9:14:37:174,0,37


VCF 2:

chr1    87708015    .   C   A   .   PASS    AN=2;DP=4;NS=1  GT:AD:DP:GQ 0/1:2,2:4:8.42


Merged VCF file:

chr1    87708015    rs58006838  C   T,A 145.77  PASS    AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.479;DB;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=3.9299;MLEAC=1;MLEAF=0.500;MQ=68.54;MQ0=0;MQRankSum=-1.109;NS=1;QD=10.41;ReadPosRankSum=0.925;set=Intersection GT:AD:DP:GQ **0/1**:3,9,2:14:37


command used:

java -jar $gatk/2.7-1-g42d771f/GenomeAnalysisTK.jar -T CombineVariants -V one.vcf.gz -V two.vcf.gz -o test.vcf -R$ref
`

Is this a known limitation or a bug?

Post edited by Geraldine_VdAuwera on
Tagged:

It looks to me like this is working properly. It's a heterozygous site in both cases. What do you think should be different?

• Member

output VCF it is not following the VCF 4.1 format and is not a valid variant according to GATK ValidateVariants walker, possible genotype values for this multi allelic variants is 0/2 1/2 2/2 right ??

Why would 0/1 not be correct? The sample is heterozygous, and the first of the ALT alleles is chosen (you can change that by specifying a different merge option if you want).

ValidateVariants is saying that it is not valid? Can you post the output?

• Member
edited September 2013

Here is the command and the error
java -jar 2.7-1-g42d771f/GenomeAnalysisTK.jar -T ValidateVariants -V variants.vcf.gz -R \$ref

##### ERROR MESSAGE: File /data2/bsi/secondary/Kocher_Jean-Pierre_m026645/whole_genome/simulated_normal_8lanes/.tmp/s_normal_8l/variant/chr1_old/variants.vcf.gz fails strict validation: one or more of the ALT allele(s) for the record at position chr1:87708015 are not observed at all in the sample genotypes

VCF line for the specific line is here :

zcat variants.vcf.gz | grep 87708015

Thanks

Saurabh