.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH SAMBLASTER: "1" "July 2018" "samblaster: Version 0.1.24" "User Commands"
.SH NAME
samblaster: \-  post processing on an aligner (eg. bwa mem):
.SH SYNOPSIS
bwa mem <idxbase> samp.r1.fq samp.r2.fq | samblaster [\-e] [\-d samp.disc.sam] [\-s samp.split.sam] | samtools view \fB\-Sb\fR \- > samp.out.bam
bwa mem \fB\-M\fR <idxbase> samp.r1.fq samp.r2.fq | samblaster \fB\-M\fR [\-e] [\-d samp.disc.sam] [\-s samp.split.sam] | samtools view \fB\-Sb\fR \- > samp.out.bam
.SH DESCRIPTION
Tool to mark duplicates and optionally output split reads and/or discordant pairs.
Input sam file must contain paired end data, contain sequence header and be sorted by read ids.
Output will be all alignments in the same order as input, with duplicates marked with FLAG 0x400.
.SS "For use with a pre-existing bam file to pull split, discordant and/or unmapped reads:"
.IP
samtools view \fB\-h\fR samp.bam | samblaster [\-a] [\-e] [\-d samp.disc.sam] [\-s samp.split.sam] [\-u samp.umc.fasta] \fB\-o\fR \fI\,/dev/null\/\fP
.SH OPTIONS
Input/Output Options:
\fB\-i\fR \fB\-\-input\fR           FILE Input sam file [stdin].
\fB\-o\fR \fB\-\-output\fR          FILE Output sam file for all input alignments [stdout].
\fB\-d\fR \fB\-\-discordantFile\fR  FILE Output discordant read pairs to this file. [no discordant file output]
\fB\-s\fR \fB\-\-splitterFile\fR    FILE Output split reads to this file abiding by parameters below. [no splitter file output]
\fB\-u\fR \fB\-\-unmappedFile\fR    FILE Output unmapped/clipped reads as FASTQ to this file abiding by parameters below. [no unmapped file output].
.TP
Requires soft clipping in input file.
Will output FASTQ if QUAL information available, otherwise FASTA.
.PP
Other Options:
\fB\-a\fR \fB\-\-acceptDupMarks\fR       Accept duplicate marks already in input file instead of looking for duplicates in the input.
\fB\-e\fR \fB\-\-excludeDups\fR          Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file.
\fB\-r\fR \fB\-\-removeDups\fR           Remove duplicates reads from all output files. (Implies \fB\-\-excludeDups\fR).
.TP
\fB\-\-addMateTags\fR
Add MC and MQ tags to all output paired\-end SAM lines.
.TP
\fB\-\-ignoreUnmated\fR
Suppress abort on unmated alignments. Use only when sure input is read\-id grouped and alignments have been filtered.
.PP
\fB\-M\fR                        Run in compatibility mode; both 0x100 and 0x800 are considered chimeric. Similar to BWA MEM \fB\-M\fR option.
.TP
\fB\-\-maxSplitCount\fR
INT Maximum number of split alignments for a read to be included in splitter file. [2]
.HP
\fB\-\-maxUnmappedBases\fR INT Maximum number of un\-aligned bases between two alignments to be included in splitter file. [50]
.TP
\fB\-\-minIndelSize\fR
INT Minimum structural variant feature size for split alignments to be included in splitter file. [50]
.TP
\fB\-\-minNonOverlap\fR
INT Minimum non\-overlaping base pairs between two alignments for a read to be included in splitter file. [20]
.TP
\fB\-\-minClipSize\fR
INT Minimum number of bases a mapped read must be clipped to be included in unmapped file. [20]
.PP
\fB\-q\fR \fB\-\-quiet\fR                Output fewer statistics.
.SH VERSION
0.1.24
.SH AUTHOR
Greg Faust (gf4ea@virginia.edu)