-.TH samtools 1 "05 July 2011" "samtools-0.1.17" "Bioinformatics tools"
+.TH samtools 1 "15 March 2013" "samtools-0.1.19" "Bioinformatics tools"
.SH NAME
.PP
samtools - Utilities for the Sequence Alignment/Map (SAM) format
.PP
bcftools view in.bcf chr2:100-200 > out.vcf
.PP
-bcftools view -vc in.bcf > out.vcf 2> out.afs
+bcftools view -Nvm0.99 in.bcf > out.vcf 2> out.afs
.SH DESCRIPTION
.PP
.B OPTIONS:
.RS
-.TP 8
+.TP 10
.B -b
Output in the BAM format.
.TP
.I FILE
[null]
.TP
+.BI -s \ FLOAT
+Fraction of templates/pairs to subsample; the integer part is treated as the
+seed for the random number generator [-1]
+.TP
.B -S
Input is in SAM. If @SQ header lines are absent, the
.B `-t'
.TP
.B tview
-samtools tview <in.sorted.bam> [ref.fasta]
+samtools tview
+.RB [ \-p
+.IR chr:pos ]
+.RB [ \-s
+.IR STR ]
+.RB [ \-d
+.IR display ]
+.RI <in.sorted.bam>
+.RI [ref.fasta]
Text alignment viewer (based on the ncurses library). In the viewer,
press `?' for help and press `g' to check the alignment start from a
region in the format like `chr10:10,000,000' or `=10,000,000' when
viewing the same reference sequence.
+.B Options:
+.RS
+.TP 14
+.BI -d \ display
+Output as (H)tml or (C)urses or (T)ext
+.TP
+.BI -p \ chr:pos
+Go directly to this position
+.TP
+.BI -s \ STR
+Display only reads from this sample or read group
+.RE
+
.TP
.B mpileup
-.B samtools mpileup
-.RB [ \-EBug ]
+samtools mpileup
+.RB [ \-EBugp ]
.RB [ \-C
.IR capQcoef ]
.RB [ \-r
.I INT
leads to more indel calls. [40]
.TP
+.BI -p
+Apply -m and -F thresholds per sample to increase sensitivity of calling.
+By default both options are applied to reads pooled from all samples.
+.TP
.BI -P \ STR
Comma dilimited list of platforms (determined by
.BR @RG-PL )
.TP
.B sort
-samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
+samtools sort [-nof] [-m maxMem] <in.bam> <out.prefix>
Sort alignments by leftmost coordinates. File
.I <out.prefix>.bam
.B -n
Sort by read names rather than by chromosomal coordinates
.TP
+.B -f
+Use
+.I <out.prefix>
+as the full output path and do not append
+.I .bam
+suffix.
+.TP
.BI -m \ INT
Approximately the maximum required memory. [500000000]
.RE
.IR mutRate ]
.RB [ \-p
.IR varThres ]
+.RB [ \-m
+.IR varThres ]
.RB [ \-P
.IR prior ]
.RB [ \-1
.BI -i \ FLOAT
Ratio of INDEL-to-SNP mutation rate [0.15]
.TP
+.BI -m \ FLOAT
+New model for improved multiallelic and rare-variant calling. Another
+ALT allele is accepted if P(chi^2) of LRT exceeds the FLOAT threshold. The
+parameter seems robust and the actual value usually does not affect the results
+much; a good value to use is 0.99. This is the recommended calling method. [0]
+.TP
.BI -p \ FLOAT
A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
.TP
CLR int Phred log ratio of genotype likelihoods with and without the trio/pair constraint
UGT string Most probable genotype configuration without the trio constraint
CGT string Most probable configuration with the trio constraint
+VDB float Tests variant positions within reads. Intended for filtering RNA-seq artifacts around splice sites
+RPB float Mann-Whitney rank-sum test for tail distance bias
+HWE float Hardy-Weinberg equilibrium test, Wigginton et al., PMID: 15789306
.TE
.SH EXAMPLES
Collecting indel candidates from reads sequenced by an indel-prone
technology may affect the performance of indel calling.
+Note that there is a new calling model which can be invoked by
+
+ bcftools view -m0.99 ...
+
+which fixes some severe limitations of the default method.
+
+For filtering, best results seem to be achieved by first applying the
+.IR SnpGap
+filter and then applying some machine learning approach
+
+ vcf-annotate -f SnpGap=n
+ vcf filter ...
+
+Both can be found in the
+.B vcftools
+and
+.B htslib
+package (links below).
+
.IP o 2
Derive the allele frequency spectrum (AFS) on a list of sites from multiple individuals:
.SH SEE ALSO
.PP
Samtools website: <http://samtools.sourceforge.net>
+.br
+Samtools latest source: <https://github.com/samtools/samtools>
+.br
+VCFtools website with stable link to VCF specification: <http://vcftools.sourceforge.net>
+.br
+HTSlib website: <https://github.com/samtools/htslib>