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)