add --output,-c option to mpileup

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 4b3f75a1926f0c4248f228f6378d2ff06e3e0c77..2762563646802321108dc811b86934de99412199 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
@@ -186,6 +186,8 @@ samtools mpileup
 .IR minBaseQ ]
 .RB [ \-q
 .IR minMapQ ]
+.RB [ \-c
+.IR Output file [stdout] ]
 .I in.bam
 .RI [ in2.bam
 .RI [ ... ]]
@@ -285,6 +287,9 @@ Output per-sample Phred-scaled strand bias P-value
 Similar to
 .B -g
 except that the output is uncompressed BCF, which is preferred for piping.
+.TP
+.BR \-c ", " \-\-output =\fIFILE\fR
+File to output bcf (vcf with \fB\-g\fR) to; default is stdout.
 
 .TP
 .B Options for Genotype Likelihood Computation (for -g or -u):
@@ -353,7 +358,7 @@ which enables fast BAM concatenation.
 
 .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
@@ -371,6 +376,13 @@ Output the final alignment to the standard output.
 .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
@@ -974,6 +986,25 @@ tag set to
 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:
 
@@ -1032,3 +1063,9 @@ specification.
 .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>