Name: bam2cram-check
Owner: Wellcome Trust Sanger Institute - Human Genetics Informatics
Description: null
Created: 2016-02-05 14:19:36.0
Updated: 2016-02-05 17:01:27.0
Pushed: 2016-10-26 10:01:44.0
Homepage: null
Size: 388
Language: Python
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This package is for checking that the file format convertion between a BAM and a CRAM leaves the data unaffected. The checks rely on the comparison between samtools stats' (CHK field), and on samtools flagstat. In addition to this both files are samtools quickcheck-ed. The stats are generated for both files. However, if there is a .stats or .flagstat file in the directory where each file is, then it will use those.
For running this you need:
on >= 3.5
ools >=1.3
Usage:
on main.py -b <bam_file> -c <cram_file> -e <err_file> --log <log_file>
Or alternatively, there is also a shell script for checking a full directory of BAMs and CRAMs by submitting as a job to LSF for each pair of files converted:
n_batch.sh <bam_dir> <cram_dir> <log_dir> <output_dir> <issues_dir>
where each BAM-CRAM conversion to be checked will have its own file in:
There is no need to create these dirs beforehands as the shell script creates them if they don't exist already.