Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Error with FastaAlternateReferenceMaker
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.
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