Retrodup
An integrated retroduplication caller based on 1) exon-exon junction and 2) discordant reads
Please refer to /Landscape and Variation of Novel Retroduplications in 26 Human Populations/.
- Create junction libraries
create_junction_library.pl -m null_mode -g genome_dir annotation_file (gencode)
- Extract unmapped reads and re-map to junctions
run_bwa.sh -o output_suffix junction_libs bam_files >& out.txt
- Call retroduplications from exon-exon junction
call_retroduplications.pl annotation_file sam_file > result.txt
- Cluster the discordant reads to discover insertion sites
samtools view bamfile gene_coor | java Cluster gene_coor2 > insertionpoints.txt