On 24 Sep 2015, at 09:06, Maria Sutton <[email protected]> wrote:
> 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.
What version of samtools are you using? (There was a bug in this area fixed in
June, but at present that only helps people building unreleased versions
themselves direct from the GitHub repository.)
> 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?
Is your fasta file available somewhere for us to have a go at debugging this?
John
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