NAME

samblaster: - post processing on an aligner (eg. bwa mem):

SYNOPSIS

bwa mem <idxbase> samp.r1.fq samp.r2.fq | samblaster [-e] [-d samp.disc.sam] [-s samp.split.sam] | samtools view -Sb - > samp.out.bam bwa mem -M <idxbase> samp.r1.fq samp.r2.fq | samblaster -M [-e] [-d samp.disc.sam] [-s samp.split.sam] | samtools view -Sb - > samp.out.bam

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.

OPTIONS

Input/Output Options: -i --input FILE Input sam file [stdin]. -o --output FILE Output sam file for all input alignments [stdout]. -d --discordantFile FILE Output discordant read pairs to this file. [no discordant file output] -s --splitterFile FILE Output split reads to this file abiding by parameters below. [no splitter file output] -u --unmappedFile FILE Output unmapped/clipped reads as FASTQ to this file abiding by parameters below. [no unmapped file output].

Requires soft clipping in input file.

Will output FASTQ if QUAL information available, otherwise FASTA.

Other Options: -a --acceptDupMarks Accept duplicate marks already in input file instead of looking for duplicates in the input. -e --excludeDups Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file. -r --removeDups Remove duplicates reads from all output files. (Implies --excludeDups).

--addMateTags

Add MC and MQ tags to all output paired-end SAM lines.

--ignoreUnmated

Suppress abort on unmated alignments. Use only when sure input is read-id grouped and alignments have been filtered.

-M Run in compatibility mode; both 0x100 and 0x800 are considered chimeric. Similar to BWA MEM -M option.

--maxSplitCount

INT Maximum number of split alignments for a read to be included in splitter file. [2]

--maxUnmappedBases INT Maximum number of un-aligned bases between two alignments to be included in splitter file. [50]

--minIndelSize

INT Minimum structural variant feature size for split alignments to be included in splitter file. [50]

--minNonOverlap

INT Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file. [20]

--minClipSize

INT Minimum number of bases a mapped read must be clipped to be included in unmapped file. [20]

-q --quiet Output fewer statistics.

VERSION

0.1.24

AUTHOR

Greg Faust (gf4ea@virginia.edu)