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sam2bam specifications


Unique identifier OMICS_16239
Name sam2bam
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data A SAM file.
Input format SAM
Output data A BAM file.
Output format BAM
Operating system Unix/Linux
Programming languages Shell (Bash)
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Takeshi Ogasawara <>

Publication for sam2bam

sam2bam in publications

PMCID: 5549768
PMID: 28749941
DOI: 10.1371/journal.pgen.1006903

[…] within”). further filters were applied to the mapped reads before conversion into bam (module filtersam with removeunmapped = true; module sortsam; module rmdupgalax with is_sort = true; module sam2bam with compression.level = 5). bigwig files were created from the resulting bam files using deeptools’ bamcoverage [] (version 1.6.0, with options:—binsize 1—normalizeto1x […]

PMCID: 3945748
PMID: 24627757
DOI: 10.12688/f1000research.1-2.v2

[…] around indels (realignertargetcreator and indelrealigner), quality score recalibration (countcovariates and tablerecalibrator) and finally variant calling (unifiedgenotyper). the wrapper scripts and are provided and can be used to recreate the processing steps from alignment files (sam format) to variant call (vcf format)., the reads and mutation panel utilized […]

sam2bam institution(s)
IBM Research-Tokyo, Tokyo, Japan; IBM Systems, Austin, TX, USA; IBM Systems, Poughkeepsie, NY, USA
sam2bam funding source(s)
Supported by IBM.

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