What is TranspoSeq-Exome?
TranspoSeq-Exome identifies somatic retrotransposon insertions in exome sequencing data.
Download source code: TranspoSeq-Exome_v1.0.tar.gz
All reference files can be found on the TranspoSeq page.
How does TranspoSeq-Exome work?
TranspoSeq-Exome consists of three steps. First, tumor and normal BAM files are parsed for split reads identified by BWA that are at least 10bp in length. These clipped portions of the read are aligned to the database of consensus retrotransposon sequences. Next, reads that pass alignment are clustered by read strand in the forward and reverse direction. Finally, clusters are gathered and assembled de novo to get longer potential contigs, which are aligned back to the database of consensus retrotransposons.