The --combined flag is causing the problem here. When it is removed, the tool executes normally.
whenever possible, a set of BAM/BED files to reproduce the issue
I am using a 40x coverage WGS NA12878 BAM and a 40x WGS NA24385 BAM. Too large to include. The problem does not present when I test small BAMs however.
version of sambamba == 0.6.8
version of samtools if the issue is with pileup tool = N/A
the command line or bash script used (feel free to shorten paths and filenames)
Outputs: sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018 LDC 1.13.0 / DMD v2.083.1 / LLVM7.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)
# chrom chromStart chromEnd readCount meanCoverage Processing reference #1 (chr1) chr1 9000 10000 12 0.014 Segmentation fault (core dumped)
The --combined flag is causing the problem here. When it is removed, the tool executes normally.