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.

   For use with a pre-existing bam file to pull split, discordant and/or unmapped reads:
              samtools   view   -h  samp.bam  |  samblaster  [-a]  [-e]  [-d  samp.disc.sam]  [-s
              samp.split.sam] [-u samp.umc.fasta] -o /dev/null

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)