Help with FastaAlternateReferenceMaker for converting VCF to fasta

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 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(
at htsjdk.variant.vcf.VCFHeader.getSequenceDictionary(

Has anyone encountered a similar issue?




Sign In or Register to comment.