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.
Samtools faidx "Segmentation fault (core dumped)"
I am preparing my fasta file so I can apply it to HaplotypeCaller. At the stage where I use samtools faidx tmp.fasta I'm getting segmentation fault (core dumped). At first it specified the errors so I got rid of the blank lines in the sequence and also the header.
Now, it just gives me that and I looked online but I couldn't find any help. Do you think it's a matter of size of the file? What should I do in such case?
Thank you very much.