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Old 03-12-2012, 01:28 PM   #1
Location: Houston, TX

Join Date: Mar 2012
Posts: 15
Default Segmentation fault (core dumped) in Samtools

Hi, All,

I want to map the RNA-seq BMA files back to the reference, and I used the samtools pileup command. It always shows the error "Segmentation fault (core dumped)".

It should not be the problem in the reference genome, because I have tried "fold" command to format the reference genome, as well as the "faidx" in samtools. They did not work. Strangely, for different BAM files, the pileup sometimes shows the error at the very beginning, some times stopped at chr6, while some other times shows the errors at chr10 or later chromosomes.

My command is "samtools view -u Inputfile (BAM) | samtools pileup -vcf hg19.fa - > output". However, when I tried Partek, it runs very well.

Anyone has any idea what is the problem with these BAM files? What I should do to fix these bugs/modify the BAM files?

Thanks a lot.
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