Bio-samtools statistics

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Bio-samtools specifications

Information


Unique identifier OMICS_08018
Name Bio-samtools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM,BAM
Output format SAM,BAM
Operating system Unix/Linux
Programming languages Ruby
License MIT License
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
BioRuby
Maintained Yes

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Documentation


Maintainer


  • person_outline Dan MacLean <>

Publications for Bio-samtools

Bio-samtools in publications

 (5)
PMCID: 5730107
PMID: 29240764
DOI: 10.1371/journal.pgen.1007098

[…] by first widening indel variants to their narrowest unambiguous region, then tallying spanning reads both with and without the indel using the perl module bio::samtools (http://search.cpan.org/~lds/bio-samtools/lib/bio/db/sam.pm). confidence interval boundaries with the highest posterior density for the estimated read allele proportions were calculated in r using cran ‘binom’ package’s […]

PMCID: 5568602
PMID: 28830520
DOI: 10.1186/s12938-017-0356-5

[…] then mapped to the corresponding transcriptome using bowtie2 [] with default parameters and the −a option to allow each read to map in all possible transcripts. mapped reads are then counted with bio-samtools from bioruby [] with the −f2 option to count only reads where both ends are mapping on the same transcript (only for illumina reads). the output is the tab-delimited, read count table […]

PMCID: 4074842
PMID: 24943349
DOI: 10.1186/1755-8794-7-36

[…] insert size lay outside a 50 bp - 500 bp interval from the tumor bam files. gatk [] is then used to generate a list of potential small indels from this bam. a customized perl script, which uses the bio-samtools library from bioperl [], takes these indel positions and for each of the indels looks at the region in the normal sample consisting of 5 bp upstream from the start and 5 bp downstream […]

PMCID: 3731364
PMID: 23936375
DOI: 10.1371/journal.pone.0070051

[…] where a number reads either start or terminate their local alignment at an internal position (). taking advantage of this property, the algorithm processes the g2t sam files (using the perl bio-samtools library v1.36), computing a p-value for every change point within a contig. low p-values indicate an unexpectedly large number of reads supporting the change point, and are suggestive […]

PMCID: 3359355
PMID: 22649506
DOI: 10.1371/journal.pone.0037029

[…] whose insert size laid outside the interval (50,500) from the tumor bam files. gatk was then used to generate a list of potential small indels from this bam. a customized perl script, which uses the bio-samtools library from bioperl , takes these indel positions and for each of the indels, looks at the region in the normal sample that is 5 bases upstream from the start of the indel and 5 bases […]


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Bio-samtools institution(s)
The Sainsbury Laboratory and The Genome Analysis Centre, Norwich Research Park, Norwich, UK
Bio-samtools funding source(s)
RHRG is funded by a Norwich Research Park PhD Studentship and a Funding and Maintenance Grant from The Genome Analysis Centre. G.J.E. and D.M. are supported by The Gatsby Charitable Foundation.

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