SortVCF in Picard

Question

[Maheswari P]

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(VCFEncoder.java:173) at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:111) at htsjdk.variant.vcf.VCFRecordCodec.encode(VCFRecordCodec.java:46) at htsjdk.variant.vcf.VCFRecordCodec.encode(VCFRecordCodec.java:18) at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:226) at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:166) at picard.vcf.SortVcf.sortInputs(SortVcf.java:168) at picard.vcf.SortVcf.doWork(SortVcf.java:101) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

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.

Answer 1

[Pierre Lindenbaum]

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