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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