SortVCF in Picard
Entering edit mode
5.8 years ago

i am working on SORTVcf picard tool. java -jar picard.jar SortVcf I=filename.vcf o=output.vcf SEQUENCE_DICTIONARY=reference.dict I am getting error as Exception in thread "main" java.lang.IllegalStateException: Key found in VariantContext field INFO at chr1:10327 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default. at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError( at htsjdk.variant.vcf.VCFEncoder.encode( at htsjdk.variant.vcf.VCFRecordCodec.encode( at htsjdk.variant.vcf.VCFRecordCodec.encode( at htsjdk.samtools.util.SortingCollection.spillToDisk( at htsjdk.samtools.util.SortingCollection.add( at picard.vcf.SortVcf.sortInputs( at picard.vcf.SortVcf.doWork( at picard.cmdline.CommandLineProgram.instanceMain( at picard.cmdline.PicardCommandLine.instanceMain( at picard.cmdline.PicardCommandLine.main(

I am working in 2.5.0 picard tool. Please any1 help me in this problem. I am beginner to this RNA seq analysis. Let know the early solution with reason of error.

RNA-Seq • 3.1k views
Entering edit mode
5.7 years ago

The message is clear: your VCF is malformed , there is a field in the INFO column (eg 'AF', 'AC' ..) which definition is missing in the VCF header. You can add it with awk...

awk '/^#CHROM/ {printf("##INFO=<ID=AAC,Number=1,Type=Integer,Description=\"Alt Allele Count\">\n");} {print;}'  input.vcf > out.vcf

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