Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
CombineGVCFs : key isn't defined in the VCFHeader
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?