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.
FastaAlternateReferenceMaker generate a reference fasta rather than my sample haplotype fasta
Hi, I am using the following command, wanting to generate haplotype fasta for 97 samples:
java -Xmx25g -jar $gatk -T FastaAlternateReferenceMaker -R $ref_genome -o new_output.fasta --variant $vcf
Here are what I did to my .vcf file:
1) I keep all the meta-information
2) I only select a specific region in my .vcf file (around SNP sites within 3Mb in the reference genome)
I attached a .zip file containing the first 120 lines of my .vcf file, I do not know how do deal with this error.
Looking forward to professional guidance, thank you!