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Error with FastaAlternateReferenceMaker

bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

Hello,

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

Best,

Christian

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