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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/.

  1. Create junction libraries -m null_mode -g genome_dir annotation_file (gencode)

  1. Extract unmapped reads and re-map to junctions -o output_suffix junction_libs bam_files >& out.txt

  1. Call retroduplications from exon-exon junction annotation_file sam_file > result.txt

  1. Cluster the discordant reads to discover insertion sites

samtools view bamfile gene_coor | java Cluster gene_coor2 > insertionpoints.txt