See http://www.broadinstitute.org/gatk/ #Genome Analysis ToolKit, Lund Oncology Department Fork

##New walkers

###SplitSAMBySoftClip Splits SAM/BAM files in two. One part with all the reads that contain soft clipping (outputRoot + "_sc.bam"). The other part contains all the reads that do not have any soft clipping in their CIGAR-strings (outputRoot + ".bam").

Example:

SAM file needs to have sort order queryname, use Picards SortSam to fix:

java -Xmx4g -jar ./picard/SortSam.jar I=aligned.bam O=aligned.querynamesorted.bam SO=queryname

Or samtools if your file is already sorted correctly but has the wrong SO header:

samtools view -H -o header.sam aligned.bam
sed -ie 's/SO\:unsorted/SO\:queryname/g' ./header.sam
samtools reheader ./header.sam aligned.bam

Split file into aligned.querynamesorted.split.bam and aligned.querynamesorted.split_sc.bam:

java -Xmx4g -jar ./GenomeAnalysisTK.jar -T SplitSAMBySoftClip -I aligned.querynamesorted.bam --outputRoot ./aligned.querynamesorted.split -R ./human_g1k_v37.fasta -U

(The tool requires GATK Unsafe mode because the sort order cannot be indexed)