bam‐readcount statistics

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Citations per year

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Protocols

bam‐readcount specifications

Information


Unique identifier OMICS_19500
Name bam‐readcount
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
License MIT License
Computer skills Advanced
Version 0..8.0
Stability Stable
Source code URL https://codeload.github.com/genome/bam-readcount/zip/v0.8.0
Maintained Yes

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bam‐readcount citations

 (10)
library_books

Punctuated evolution of canonical genomic aberrations in uveal melanoma

2018
Nat Commun
PMCID: 5760704
PMID: 29317634
DOI: 10.1038/s41467-017-02428-w

[…] rporated local realignment that adjusts for tumors with purity less than 100%, multiple subclones, and/or copy number variation (either local or aneuploidy). Varscan2 output was further refined using bam-readcount and a false positive filter (fplfilter) with filter parameters set based on the TCGA-ICGC DREAM-3 SNV Challenge results, with adjustment of minimum average read trim length. For MuTect2, […]

library_books

The effects of transcription and recombination on mutational dynamics of short tandem repeats

2017
Nucleic Acids Res
PMCID: 5814968
PMID: 29300948
DOI: 10.1093/nar/gkx1253

[…] e Y55 reference sequence using Bowtie 2 () with ‘sensitive’ settings and the constraint that no read should align to more than one location. Coverage for each microsatellite was then calculated using Bam-readcount (https://github.com/genome/bam-readcount).The locations of replication origins (autonomously replicating sequences) were downloaded from the Saccharomyces DNA Replication Origin Database […]

call_split

Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations

2017
Nat Commun
PMCID: 5688099
PMID: 29142225
DOI: 10.1038/s41467-017-01730-x
call_split See protocol

[…] For all TCGA and Chinese samples, we obtained the read coverage information of exonic common SNPs in the dbSNP (build 147) using bam-readcount (https://github.com/genome/bam-readcount) for each normal sample. The minimum base quality was set to 15, and our analysis included 168,275 common SNPs with the coverage of ≥8 in each sa […]

library_books

Visualizing adenosine to inosine RNA editing in single mammalian cells

2017
Nat Methods
PMCID: 5542810
PMID: 28604724
DOI: 10.1038/nmeth.4332

[…] icates (MarkDuplicates). We then trimmed 5′ ends of all aligned and PCR-deduplicated reads with bamUtil v1.0.13 (http://genome.sph.umich.edu/wiki/BamUtil. Accessed: 28th October 2016). Finally, using bam-readcount v we filtered aligned reads by those overlapping candidate editing sites of interest, by their overall mapping (phred) score and individual base call qualities using a custom bed file an […]

library_books

Prediction and prioritization of neoantigens: integration of RNA sequencing data with whole‐exome sequencing

2017
Cancer Sci
PMCID: 5329159
PMID: 27960040
DOI: 10.1111/cas.13131

[…] total mapped reads in RNA‐Seq were 76.0 M and 62.6 M, respectively. Expression values were calculated as FPKM using Cufflinks (version 2.0.2). The RNA read count at each mutation site was obtained by bam‐readcount (https://github.com/genome/bam-readcount). […]

library_books

Spatial intratumor heterogeneity of genetic, epigenetic alterations and temporal clonal evolution in esophageal squamous cell carcinoma

2016
Nat Genet
PMCID: 5127772
PMID: 27749841
DOI: 10.1038/ng.3683

[…] least one tumor region, a method described by Stachler et al. was used to increase the sensitivity of detecting these mutations in other tumor regions from the same individual with low VAF. In brief, Bam-Readcount (URL) was used to obtain read counts for unique somatic variants across all tumor regions. A variant was considered as absent if either its VAF was less than 0.02 or the reads were fewer […]


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