I'm trying to run samtools mpileup on BAM files, part of a tumour/normal pair so I can do some further analysis.
BAM's are aligned with BWA, post-processed with GATK and validated with ValidateSam from Picard. As far as I can tell there is no difference really between the BAM files, except that one causes mpileup to segfault every time.
I don't really know how to diagnose why this is happening - any hints? Errors occuring with Version: 0.1.18 (r982:295) and 0.1.14.
BAM's are aligned with BWA, post-processed with GATK and validated with ValidateSam from Picard. As far as I can tell there is no difference really between the BAM files, except that one causes mpileup to segfault every time.
I don't really know how to diagnose why this is happening - any hints? Errors occuring with Version: 0.1.18 (r982:295) and 0.1.14.
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