bam‐readcount statistics

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Citations per year

Number of citations per year for the bioinformatics software tool bam‐readcount

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bam‐readcount specifications


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
Maintained Yes




No version available


bam‐readcount citations


Punctuated evolution of canonical genomic aberrations in uveal melanoma

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, […]


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

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 ( locations of replication origins (autonomously replicating sequences) were downloaded from the Saccharomyces DNA Replication Origin Database […]


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

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 ( 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 […]


Visualizing adenosine to inosine RNA editing in single mammalian cells

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 ( 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 […]


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

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 ( […]


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

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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