+ mpileup samtools mpileup [-Bug] [-C capQcoef] [-r reg] [-f in.fa] [-l
+ list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam
+ [...]]
+
+ Generate BCF or pileup for one or multiple BAM files. Align-
+ ment records are grouped by sample identifiers in @RG header
+ lines. If sample identifiers are absent, each input file is
+ regarded as one sample.
+
+ OPTIONS:
+
+ -B Disable probabilistic realignment for the computation
+ of base alignment quality (BAQ). BAQ is the Phred-
+ scaled probability of a read base being misaligned.
+ Applying this option greatly helps to reduce false
+ SNPs caused by misalignments.
+
+ -C INT Coefficient for downgrading mapping quality for reads
+ containing excessive mismatches. Given a read with a
+ phred-scaled probability q of being generated from
+ the mapped position, the new mapping quality is about
+ sqrt((INT-q)/INT)*INT. A zero value disables this
+ functionality; if enabled, the recommended value for
+ BWA is 50. [0]
+
+ -e INT Phred-scaled gap extension sequencing error probabil-
+ ity. Reducing INT leads to longer indels. [20]
+
+ -f FILE The reference file [null]
+
+ -g Compute genotype likelihoods and output them in the
+ binary call format (BCF).
+
+ -h INT Coefficient for modeling homopolymer errors. Given an
+ l-long homopolymer run, the sequencing error of an
+ indel of size s is modeled as INT*s/l. [100]
+
+ -l FILE File containing a list of sites where pileup or BCF
+ is outputted [null]
+
+ -o INT Phred-scaled gap open sequencing error probability.
+ Reducing INT leads to more indel calls. [40]
+
+ -P STR Comma dilimited list of platforms (determined by @RG-
+ PL) from which indel candidates are obtained. It is
+ recommended to collect indel candidates from sequenc-
+ ing technologies that have low indel error rate such
+ as ILLUMINA. [all]
+
+ -q INT Minimum mapping quality for an alignment to be used
+ [0]
+
+ -Q INT Minimum base quality for a base to be considered [13]
+
+ -r STR Only generate pileup in region STR [all sites]
+
+ -u Similar to -g except that the output is uncompressed
+ BCF, which is preferred for piping.
+
+
+ reheader samtools reheader <in.header.sam> <in.bam>
+
+ Replace the header in in.bam with the header in
+ in.header.sam. This command is much faster than replacing
+ the header with a BAM->SAM->BAM conversion.
+
+
+ sort samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>