Update 'samtools depad' help text regarding FASTA reference file

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 118a6e83079bddd9787e89673d64e7a4b1ddd0b3..5923abd52608ee9003cbe17c49e93755f67a647f 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "2 September 2011" "samtools-0.1.18" "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
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format


@@ -30,7 +30,7 @@ bcftools index in.bcf
 .PP
 bcftools view in.bcf chr2:100-200 > out.vcf
 .PP
 .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
 
 .SH DESCRIPTION
 .PP


@@ -140,17 +140,38 @@ to another samtools command.
 
 .TP
 .B tview
 
 .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.
 
 
 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
 .TP
 .B mpileup

-.B samtools mpileup
-.RB [ \-EBug ]
+samtools mpileup
+.RB [ \-EBugp ]

 .RB [ \-C
 .IR capQcoef ]
 .RB [ \-r
 .RB [ \-C
 .IR capQcoef ]
 .RB [ \-r


@@ -297,6 +318,10 @@ Phred-scaled gap open sequencing error probability. Reducing
 .I INT
 leads to more indel calls. [40]
 .TP
 .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 )
 .BI -P \ STR
 Comma dilimited list of platforms (determined by
 .BR @RG-PL )


@@ -577,6 +602,8 @@ Minimum base quality to be used in het calling. [13]
 .IR mutRate ]
 .RB [ \-p
 .IR varThres ]
 .IR mutRate ]
 .RB [ \-p
 .IR varThres ]

+.RB [ \-m
+.IR varThres ]

 .RB [ \-P
 .IR prior ]
 .RB [ \-1
 .RB [ \-P
 .IR prior ]
 .RB [ \-1


@@ -659,6 +686,12 @@ Call per-sample genotypes at variant sites (force -c)
 .BI -i \ FLOAT
 Ratio of INDEL-to-SNP mutation rate [0.15]
 .TP
 .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
 .BI -p \ FLOAT
 A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
 .TP


@@ -818,6 +851,9 @@ RP  int     # permutations yielding a smaller PCHI2
 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
 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
 .TE
 
 .SH EXAMPLES


@@ -945,6 +981,25 @@ tag set to
 Collecting indel candidates from reads sequenced by an indel-prone
 technology may affect the performance of indel calling.
 
 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:
 
 .IP o 2
 Derive the allele frequency spectrum (AFS) on a list of sites from multiple individuals:
 


@@ -1003,3 +1058,9 @@ specification.
 .SH SEE ALSO
 .PP
 Samtools website: <http://samtools.sourceforge.net>
 .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>