POPBAM specifications


Unique identifier OMICS_01559
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
Computer skills Advanced
Stability Stable
Maintained No


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Publication for POPBAM

POPBAM in publications

PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] the individual deduplicated bam files of re-sequenced isolates were merged by samtools v.1.2 [] to calculate genome-wide nucleotide diversity and tajima’s d in non-overlapping 5 kb windows using popbam v.3.0 (−m 10, −× 200, −q 40) []. based on the distribution of d-value, outlier windows (d-value <5th or > 95th percentile) were selected. genes with at least 80% of their length […]

PMCID: 4578789
PMID: 26391223
DOI: 10.1186/s12862-015-0472-4

[…] data in the ncbi short read archive []. reads are mapped to the genome of the reference d. melanogaster strain y1;cn1bw1sp1 (version 5.45) using the bwa software []. variants are called using the popbam software with default settings []. gene alignments are then constructed for the longest transcript per gene from the flybase mrna annotations, using the perl script pbsnp2fa.pl […]

PMCID: 4396994
PMID: 25874895
DOI: 10.1371/journal.pone.0118621

[…] alignments for individual lines in the bam format were merged using the samtools software package []. the values of f st and g min were calculated in non-overlapping 50 kb windows using the popbam software package []. we only analyzed nucleotide sites that met the following criteria: read depth per line greater than 5, phred-scaled scores for the minimum root-mean squared mapping […]

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POPBAM institution(s)
Department of Biology, University of Rochester, Chinahester, NY, USA

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