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CombineGVCFs : key isn't defined in the VCFHeader

Hi there,

I am trying to combine gVCFs using CombineGVCFs and get the error: "Key END found in VariantContext field INFO at chr1:10439 but this key isn't defined in the VCFHeader".

The gVCFs are generated using HaplotypeCaller GATK4:
gatk --java-options "-Xmx50G" HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I x.bam -O x.g.vcf.gz

In the gVCF headers are "contig=<ID=chr1,length=248956422>" and the position "chr1 10439 . AC A 359.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.836;ClippingRankSum=0.000;DP=36;ExcessHet=3.0103;FS=2.063;MLEAC=1;MLEAF=0.500;MQ=37.15;MQRankSum=0.425;QD=12.85;ReadPosRankSum=-0.401;SOR=1.445 GT:AD:DP:GQ:PL 0/1:7,21:28:99:397,0,129"

My question is: What Key is the error referring to (maybe: contig=<ID=chr1,length=248956422>) and how should it be defined in the header giving the above position?

Is there any obvious solution to this?

Thanks you!

Best Answer


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