GitHub - joshwaterfall/RetroSeq: RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.

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RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.

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RetroSeq: A tool for discovery and genotyping of transposable elements from short read alignments
Version: 0.1
Author: Thomas Keane (thomas.keane@sanger.ac.uk)

Usage: retroseq.pl -<command> options

            -discover       Takes a BAM and a set of reference TE (fasta) and calls candidate supporting read pairs (BED output)
            -call           Takes multiple output of discovery stage (can be multiple files of same sample e.g. multiple lanes) and a BAM and outputs a VCF of TE calls
            -genotype       Input is a VCF of TE calls and a set of sample BAMs, output is a new VCF with genotype calls for new samples
            
NOTE: retroseq.pl requires samtools, exonerate, unix sort to be in the default path

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RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.

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