Question: bcftools merge segmentation fault?
gravatar for atruong
6.0 years ago by
United States
atruong20 wrote:

I'm attempting to run bcftools, specifically the merge function, on a set of 152 vcf files (all properly processed and indexed). However, I'm not satisfied with the default headers that were generated by the merge, so I wanted to provide a file containing the headers I want instead. However, whenever I execute, I keep getting "Segmentation fault (core dumped)". My command is as follows:

./bcftools merge --use-header header.txt --print-header -O v -l file.txt

(--print-header is just for me to check that the setting stuck) The command runs fine if I don't specify my own header file. However, when I do, I receive the above error. Is there any way for me to address this?

(I'm aware of a similar topic Joinx Vcf-Merge Produces A Segmentation Fault Before Merging Is Complete that asks a similar question, but he's using a different tool, and his solution also appears to be tool-specific. I suppose I could switch tools for the merge, but I would like to see if I could resolve this first.)

I'm using 64-bit Red Hat Enterprise. I can provide more information if necessary.

bcftools software error • 2.5k views
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by atruong20
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