Hi, I'm new to this forum and I guess I would like to post this question here.
I had an aligned bam file with reads from 3 PacBio SMRT runs using blasr.
When I try to call snp between the bam and another bam file from illumina reads from the same library using "samtools mpileup -u". It raised an error with segmentation fault(core dump).
The error seems to originate from the pacbio bam file since doing mpileup with the illumina bam file alone, it finishes without error.
The pacbio bam file is sorted and when I try to index the bam, it also finishes without error. Later I tried mpileup without -u option, the text pileup finishes OK.
Could anyone give me some hints or directions to debug this issue?
Best,
jack
I had an aligned bam file with reads from 3 PacBio SMRT runs using blasr.
When I try to call snp between the bam and another bam file from illumina reads from the same library using "samtools mpileup -u". It raised an error with segmentation fault(core dump).
The error seems to originate from the pacbio bam file since doing mpileup with the illumina bam file alone, it finishes without error.
The pacbio bam file is sorted and when I try to index the bam, it also finishes without error. Later I tried mpileup without -u option, the text pileup finishes OK.
Could anyone give me some hints or directions to debug this issue?
Best,
jack
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