Comments (2)
can you re-index your cram with the latest samtools? There was a bug in the cram indexing in samtools discovered by indexcov that was fixed recently.
If you still see the error after that, can you share the .crai via email?
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Precompiled version was failing and after compiling the source version it worked.
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Related Issues (20)
- Differential header stringency depending on file format HOT 4
- goleft depth sliding window analysis HOT 1
- Feature request: New option --exclude for indexsplit HOT 1
- indexcov support for csi indexes HOT 2
- ndexcv: excluding chromosome: NC_031965 because of exclude-pattern: ^chrEBV$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d HOT 2
- goleft_linux64 covstats error: panic: EOF HOT 7
- coverage of the customized genome HOT 2
- error: bam is required HOT 4
- link to golang typo
- suggestion: zoomable chromosome depth plots in indexcov HOT 1
- indexcov shows stepwise coverage distribution HOT 4
- Feature request: New option --exclude for covstats HOT 2
- Indexcov errors HOT 2
- error on depth, seems to make temp file it can't find
- Negative alnSpan error HOT 2
- No longer possible to build from source or include in a Docker image HOT 2
- Running Indexcov on cram files with different paths HOT 2
- What is the value of the insert size ? HOT 2
- indexcov: usage with long reads ? HOT 1
- Indexcov searching for cram.bai HOT 1
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