.TP 10
.B view
-samtools view [-bhuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
+samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]]
Extract/print all or sub alignments in SAM or BAM format. If no region
.B `-t'
option is required.
.TP
+.B -c
+Instead of printing the alignments, only count them and print the
+total number. All filter options, such as
+.B `-f',
+.B `-F'
+and
+.B `-q'
+, are taken into account.
+.TP
.BI -t " FILE"
This file is TAB-delimited. Each line must contain the reference name
and the length of the reference, one line for each distinct reference;
tags in the
.B @RG
header lines. Individuals can be pooled in one alignment file; one
-individual can also be separated into multiple files. Similarly, one may
-consider to apply
+individual can also be separated into multiple files. In addition, one
+may consider to apply
.B -C50
to
.BR mpileup .
-SNP calling in this way also works for single sample and has the
+
+SNP calling with mpileup also works for single sample and has the
advantage of enabling more powerful filtering. The drawback is the lack
of short indel calling, which may be implemented in future.
.B calmd
command also comes with the
.B -C
-option, the same as the on in
+option, the same as the one in
.B pileup
and
.BR mpileup .
.PP
Heng Li from the Sanger Institute wrote the C version of samtools. Bob
Handsaker from the Broad Institute implemented the BGZF library and Jue
-Ruan from Beijing Genomics Institute wrote the RAZF library. Various
-people in the 1000 Genomes Project contributed to the SAM format
+Ruan from Beijing Genomics Institute wrote the RAZF library. John
+Marshall and Petr Danecek contribute to the source code and various
+people from the 1000 Genomes Project have contributed to the SAM format
specification.
.SH SEE ALSO