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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

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BAMStats in publications

 (8)
PMCID: 5906580
PMID: 29670134
DOI: 10.1038/s41598-018-24400-4

[…] 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. )., snvs and small insertions/deletions (indels) were identified using samtools mpileup (v.1.3), followed by bcftools call (v.1.3). the following parameters […]

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

[…] 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 […]

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

[…] 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) […]

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

[…] 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 […]

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 […]


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