Incorporate patches by Marcel Martin for read counting.

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 77b5a22f62b6233f513d5695ad98a61d5474cdff..7de9857245ca6debe24abaa4d6786f942886035e 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -47,7 +47,7 @@ entire alignment file unless it is asked to do so.
 
 .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
@@ -100,6 +100,15 @@ Input is in SAM. If @SQ header lines are absent, the
 .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;
@@ -601,12 +610,16 @@ Individuals are identified from the
 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 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.
+
 .IP o 2
 Derive the allele frequency spectrum (AFS) on a list of sites from multiple individuals:
 
@@ -637,7 +650,7 @@ tags at the same time. The
 .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 .
@@ -663,8 +676,9 @@ although a little slower.
 .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