Hi,
I've a problem with a VCF when combiningGVCFs, gatk/v3.4. "headerKey END found in VariantContext field INFO at chr2L:64003 but this key isn't defined in the VCFHeader"
HaplotypeCaller
-nct 30 --analysis_type HaplotypeCaller --reference_sequence ../../reference_sequences/dmel/v6.0/dm6.fa \
--input_file ../../read_mapping/reference_line/RGnb/RGnb.bam \
--variant_index_type LINEAR --variant_index_parameter 128000 -mbq 10 -L chr2L \
--out ../../read_mapping/reference_line/RGnb/RGnb.g.vcfVCF
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RGnb
chr2L 43265 . A G 2147.77 . AC=2;AF=1.00;AN=2;DP=54;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.59;SOR=1.118 GT:AD:DP:GQ:PL 1/1:0,54:54:99:2176,162,0
chr2L 64003 . GT G 57.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.987;ClippingRankSum=-0.189;DP=45;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.85;MQRankSum=0.525;QD=1.28;ReadPosRankSum=1.149;SOR=0.622 GT:AD:DP:GQ:PL 0/1:25,8:33:95:95,0,521
Combine three gvcfs
--analysis_type CombineGVCFs --reference_sequence ../../reference_sequences/dmel/v6.0/dm6.fa \
--variant rg_GVCF.list --out ./RG.g.vcfError message:
java.lang.IllegalStateException: Key END found in VariantContext field INFO at chr2L:64003 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF
Previous issues for "key isn't defined in the VCFHeader"
http://gatkforums.broadinstitute.org/discussion/3962/genotypeandvalidate-error-key-callstatus-found-in-variantcontext-field-info#latest
http://gatkforums.broadinstitute.org/discussion/2331/select-variants-says-vcf-header-is-missing
https://github.com/charite/jannovar/issues/70
https://groups.google.com/forum/#!topic/gawed-awesome-analyzers/RjXtIuYQ_V8
Could anyone advise me on how to fix this?
Sincerely,
Blue