Content-type: text/html Man page of popbam

popbam

Section: Bioinformatics tools (1)
Updated: September 08 2011
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NAME

popbam - Tools for evolutionary analysis of BAM files

 

SYNOPSIS

popbam snp -f ref.fasta aln.sorted.bam chrX:1000000-2000000

 

DESCRIPTION

Popbam is a program to perform a suite of evolutionary-based analyses of SAM/BAM files which contain reads from multiple samples. Popbam relies upon the SAMtools API for processing of the pileup data structure. Popbam also requires the inclusion of the `PO' tag in the read group header line, which identifies the population from which a particular sample originates. Once the `PO' tag is included, popbam can do statistical analyses of nucleotide variation both within and between populations.

 

POPBAM COMMANDS AND OPTIONS

snp
popbam snp [-iv] [-f in.fa] [-m minCov] [-x maxCov] [-q minRmsQ] [-s minSnpQ] [-a minBaseQ] [-b minBaseQ] in.bam [region [...]]

Output consensus base calls for each sample in the BAM file. If no region is specified, all sites will be analyzed, however if the user asks for sliding window mode, a region must be specified. The format for the region designation can be: `chrX' (the entirety of chrX), `chrX:1000000' (region starting from position 1,000,000) or `chr2:1000000-2000000' (region between positions 1,000,000 and 2,000,000 bp including the end points).

OPTIONS:

-i
Quality scores are in Illumina 1.3+ format [Sanger]
-v
Output variable sites only [All sites]
-f FILE
The fastA reference file for the BAM assembly
-m INT
Minimum number of reads covering individual postions per sample [3]
-x INT
Maximum number of reads covering individual postions per sample [255]
-q INT
Minimum root mean square mapping quality for an alignment to be used [25]
-s INT
Minimum SNP quality for a site to be considered variable [25]
-a INT
Minimum mapping quality to include a read in the pileup [13]
-b INT
Minimum base quality to include a read in the pileup [13]

fasta
popbam fasta [-iv] [-f in.fa] [-m minCov] [-x maxCov] [-q minRmsQ] [-s minSnpQ] [-a minBaseQ] [-b minBaseQ] in.bam [region [...]]

Output fasta formated alignment of all samples in the BAM file.

OPTIONS:

-i
Quality scores are in Illumina 1.3+ format [Sanger]
-v
Output variable sites only [All sites]
-f FILE
The fastA reference file for the BAM assembly
-m INT
Minimum number of reads covering individual postions per sample [3]
-x INT
Maximum number of reads covering individual postions per sample [255]
-q INT
Minimum root mean square mapping quality for an alignment to be used [25]
-s INT
Minimum SNP quality for a site to be considered variable [25]
-a INT
Minimum mapping quality to include a read in the pileup [13]
-b INT
Minimum base quality to include a read in the pileup [13]

tree
popbam tree [-i] [-w winSize] [-d dist] [-f in.fa] [-m minCov] [-x maxCov] [-q minRmsQ] [-s minSnpQ] [-a minBaseQ] [-b minBaseQ] in.bam [region [...]]

Output neighbor-joining (NJ) trees in newick format of all samples in the BAM file.

OPTIONS:

-i
Quality scores are in Illumina 1.3+ format [Sanger]
-d STR
Distance: pdist (p-distance) or jc (Jukes-Cantor) [pdist]
-w INT
Use sliding window of given size (kb) [1]
-f FILE
The fastA reference file for the BAM assembly
-m INT
Minimum number of reads covering individual postions per sample [3]
-x INT
Maximum number of reads covering individual postions per sample [255]
-q INT
Minimum root mean square mapping quality for an alignment to be used [25]
-s INT
Minimum SNP quality for a site to be considered variable [25]
-a INT
Minimum mapping quality to include a read in the pileup [13]
-b INT
Minimum base quality to include a read in the pileup [13]

nucdiv
popbam nucdiv [-i] [-w winSize] [-f in.fa] [-m minCov] [-x maxCov] [-q minRmsQ] [-s minSnpQ] [-a minBaseQ] [-b minBaseQ] in.bam [region [...]]

Computes nucleotide diversity both within and between populations.

OPTIONS:

-i
Quality scores are in Illumina 1.3+ format [Sanger]
-w INT
Use sliding window of given size (kb) [1]
-f FILE
The fastA reference file for the BAM assembly
-m INT
Minimum number of reads covering individual postions per sample [3]
-x INT
Maximum number of reads covering individual postions per sample [255]
-q INT
Minimum root mean square mapping quality for an alignment to be used [25]
-s INT
Minimum SNP quality for a site to be considered variable [25]
-a INT
Minimum mapping quality to include a read in the pileup [13]
-b INT
Minimum base quality to include a read in the pileup [13]

ld
popbam ld [-i] [-w winSize] [-f in.fa] [-m minCov] [-x maxCov] [-q minRmsQ] [-s minSnpQ] [-a minBaseQ] [-b minBaseQ] in.bam [region [...]]

Computes Wall's B statistic as a measure of linkage disequilibrium within all populations.

OPTIONS:

-i
Quality scores are in Illumina 1.3+ format [Sanger]
-w INT
Use sliding window of given size (kb) [1]
-f FILE
The fastA reference file for the BAM assembly
-m INT
Minimum number of reads covering individual postions per sample [3]
-x INT
Maximum number of reads covering individual postions per sample [255]
-q INT
Minimum root mean square mapping quality for an alignment to be used [25]
-s INT
Minimum SNP quality for a site to be considered variable [25]
-a INT
Minimum mapping quality to include a read in the pileup [13]
-b INT
Minimum base quality to include a read in the pileup [13]

fspec
popbam fspec [-i] [-w winSize] [-f in.fa] [-m minCov] [-x maxCov] [-q minRmsQ] [-s minSnpQ] [-a minBaseQ] [-b minBaseQ] in.bam [region [...]]

Computes summaries of the frequency spectrum of mutations within populations. Both Tajima's D and Fay and Wu's H are calculated.

OPTIONS:

-i
Quality scores are in Illumina 1.3+ format [Sanger]
-w INT
Use sliding window of given size (kb) [1]
-f FILE
The fastA reference file for the BAM assembly
-m INT
Minimum number of reads covering individual postions per sample [3]
-x INT
Maximum number of reads covering individual postions per sample [255]
-q INT
Minimum root mean square mapping quality for an alignment to be used [25]
-s INT
Minimum SNP quality for a site to be considered variable [25]
-a INT
Minimum mapping quality to include a read in the pileup [13]
-b INT
Minimum base quality to include a read in the pileup [13]

 

LIMITATIONS

o
Popbam assumes that all samples are haploid, therefore no heterozygous consensus bases are called.
o
If any single sample does not meet the required coverage or map quality criteria, the entire alignment for that site is skipped over by popbam.
o
Popbam does not consider sites with indels.

 

AUTHOR

Dan Garrigan from the University of Rochester wrote the fundamental code for popbam. Jeff Fuller from the University of Rochester has converted much of the original code from C to C++.

 

SEE ALSO

Popbam website: <http://popbam.sourceforge.net>


 

Index

NAME
SYNOPSIS
DESCRIPTION
POPBAM COMMANDS AND OPTIONS
LIMITATIONS
AUTHOR
SEE ALSO

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Time: 17:45:12 GMT, September 08, 2011