We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Error with FastaAlternateReferenceMaker

bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin


I am having some trouble running the FastaAlternateReferenceMaker tool to convert my vcf sequences to fasta using a reference genome. I started with a multi-sequence vcf made from whole genome paired-end Illumina data. I then subset the the larger vcf file to isolate a single gene region and further subset it to only include organisms from one population. I was able to troubleshoot several issues but there seems to be something I am missing. I am no longer getting a clear error message as I was before, the message now is mostly incomprehensible except for one line which says
"htsjdk.tribble.TribbleException: Contig CAE1 does not have a length field.
at htsjdk.variant.vcf.VCFContigHeaderLine.getSAMSequenceRecord(VCFContigHeaderLine.java:80)
at htsjdk.variant.vcf.VCFHeader.getSequenceDictionary(VCFHeader.java:206)

it then goes on to list many more. I tried to use but that did not seem to work either
java -jar picard.jar FixVcfHeader -I VBOA1003.vcf.gz -O VBOA1003_Fixed.vcf.g
I could use some advice



Sign In or Register to comment.