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BAMStats specifications

Information


Unique identifier OMICS_01034
Name BAMStats
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Medium
Version 1.25
Stability Beta
Maintained Yes

Versioning


No version available

BAMStats citations

 (10)
library_books

Detection of functional protein domains by unbiased genome wide forward genetic screening

2018
Sci Rep
PMCID: 5906580
PMID: 29670134
DOI: 10.1038/s41598-018-24400-4

[…] plicates were marked by using Picard Tools (Picard version 1.128). The quality of the sequencing data post-alignment was assessed by using SAMtools stats and SAMtools flagstats (1.1+htslib−1.1), plot-bamstats, bamcheck and plot-bamcheck (Fig. ). […]

library_books

Ubiquitin C terminal hydrolase isozyme L1 is associated with shelterin complex at interstitial telomeric sites

2017
PMCID: 5681776
PMID: 29126443
DOI: 10.1186/s13072-017-0160-2

[…] ectively. We also analyzed three samples of 19,524,349 sequence reads of the SOLiD ChIP-seq data from NCBI GEO (GSE26005). All these sequences were ensured by quality check (noise to signal ratio and bamStats after mapping). The sequence reads were mapped on the human reference genome (hg19) using Lifescope v2.5.1 software (Life Technologies) with 2-mismatch settings. The GSE26005 sequences were m […]

library_books

Identification of genome wide targets of Olig2 in the adult mouse spinal cord using ChIP Seq

2017
PLoS One
PMCID: 5648140
PMID: 29049317
DOI: 10.1371/journal.pone.0186091

[…] regions. Custom input parameters were entered for reference genome (UCSC mouse genome; mm10) and fragment size (148 bp; Average ChIP fragment size as determined using BaseSpace BWA Aligner v1.1.4 and BAMStats 1.25; https://sourceforge.net/projects/bamstats/). Samples for both ChIP’d, and Input Control libraries were used as inputs for MACS2 to improve spatial resolution (specificity) of ChIP-regio […]

library_books

The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk

2017
PMCID: 5466608
PMID: 28649662
DOI: 10.1038/s41523-017-0024-8

[…] FASTQ files were de-multiplexed to individual forward and reverse files. Initial QC was performed using the FASTQC tool kit. Read alignment was performed using BWA and statistics were generated using bamstats. The human reference GRCh37 with the addition of decoy regions V5 for improving alignment accuracy and speed was used in all cases. Sixty-one samples with low quality were removed using the s […]

library_books

Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics

2017
BMC Genomics
PMCID: 5418769
PMID: 28472937
DOI: 10.1186/s12864-017-3709-3

[…] . To estimate the sequencing depth of each base, Bowtie v. 1.0.0 was used to align Illumina reads onto the assembled mitogenomes. Aligned reads were viewed using IGV, Tablet, PysamStats (v. 0.84) and BAMStats (v. 1.25) [–]. Heteroplasmic sites were identified using three conditions: first, different nucleotides were sequenced in the same position; second, that position must have more than 100 supp […]

library_books

The Dockstore: enabling modular, community focused sharing of Docker based genomics tools and workflows

2017
F1000Res
PMCID: 5333608
PMID: 28344774
DOI: 10.5256/f1000research.10919.r19471

[…] formats (in WDL or CWL) mean that the tool or workflow is self-documenting, easing the documentation burden on developers. Example Dockerfile, CWL-descriptor, and JSON parameterization files for the BAMStats ( http://bamstats.sourceforge.net) tool can be found in the ( ). As an outcome of registering their tools/workflows on Dockstore, developers can take advantage of the underlying GA4GH Tool R […]

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