https://github.com/gersteinlab/retrodup

An integrated retroduplication caller based on 1) exon-exon junction and 2) discordant reads
https://github.com/gersteinlab/retrodup

retroduplication sv

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An integrated retroduplication caller based on 1) exon-exon junction and 2) discordant reads

• Host: GitHub
• URL: https://github.com/gersteinlab/retrodup
• Owner: gersteinlab
• Created: 2017-04-14T16:51:40.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2017-04-20T02:42:53.000Z (about 8 years ago)
• Last Synced: 2025-01-20T12:07:45.674Z (4 months ago)
• Topics: retroduplication, sv
• Language: Perl
• Homepage:
• Size: 11.7 KB
• Stars: 2
• Watchers: 23
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# 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*/. 

1. Create junction libraries

`create_junction_library.pl -m null_mode -g genome_dir annotation_file (gencode)`

2. Extract unmapped reads and re-map to junctions

`run_bwa.sh -o output_suffix junction_libs bam_files >& out.txt`

3. Call retroduplications from exon-exon junction

`call_retroduplications.pl annotation_file sam_file > result.txt`

4. Cluster the discordant reads to discover insertion sites	

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