-.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
.IR minBaseQ ]
.RB [ \-q
.IR minMapQ ]
+.RB [ \-c
+.IR Output file [stdout] ]
.I in.bam
.RI [ in2.bam
.RI [ ... ]]
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):
.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
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>