Thanks for the quick reply! My bam-files are indeed bam-files, the idxstats works fine. I tried samtools bedcov from the command line (version 1.2), without the '-Q' option it works fine but if I add this option I get the same error message, so it seems to be a samtools-related error indeed...
I was mostly interested in the batch option from CNVkit, is it also possible to run this while circumventing the -Q?
Just to be sure, the command I used for the coverage analysis:
python cnvkit.py coverage ~/Documents/CNVkit/testT_dedup.realigned.bam ~/Documents/genomes/design_test4.bed -o ~/Documents/CNVkit/test_dedup.realigned.cnn
Processing reads in testT_dedup.realigned.bam
[E::hts_open] fail to open file '-Q'
Segmentation fault: 11
[E::hts_open] fail to open file '-Q'
Segmentation fault: 11
python cnvkit.py batch ~/Documents/CNVkit/*T_dedup.realigned.bam --normal ~/Documents/CNVkit/*R*bam --fasta ~/Documents/genomes/GRCh37_gatk.fasta --access ~/bin/cnvkit/data/access-10kb.hg19_noChr.bed --output-reference ~/Documents/CNVkit/test.cnn --output-dir ~/Documents/test/ -t ~/Documents/genomes/design_test4.bed
Detected file format: BED
Detected file format: BED
Detected file format: BED
Wrote /Users/.../Documents/CNVkit/test/design_test4.antitarget.bed with 1678 background intervals
Building a copy number reference from normal samples...
Processing reads in test1R_dedup.realigned.bam
[E::hts_open] fail to open file '-Q'
Segmentation fault: 11
Detected file format: BED
Detected file format: BED
Wrote /Users/.../Documents/CNVkit/test/design_test4.antitarget.bed with 1678 background intervals
Building a copy number reference from normal samples...
Processing reads in test1R_dedup.realigned.bam
[E::hts_open] fail to open file '-Q'
Segmentation fault: 11
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