alu-detect

About

alu-detect is a tool that combines read-pair and split-read information in order to detect novel Alus and their precise breakpoints directly from either whole-genome or whole-exome sequencing data, while also identifying insertions directly in the vicinity of existing Alus.

For detailed information, see the README file.

Citatations

News

05 May 2013. Added wrapper script to access main functionality. Various other fixes.

28 Jan 2013. Major rewrite of the internal read naming scheme. This addresses 2 issues: high disk space usage during progressive mapping, and possible crashes for reads longer than 120bp. The new executables are incompatible with the old data files. To convert, e.g., reads.to_remap files from the old format to the new format, use fq-update-clone-names.

18 Jan 2013. Inhibit the saving of discordant reads prior to trimming and renaming, saving disk space.

10 Jan 2013. Fixed issue causing a crash when some chromosomes (e.g. chrM) are indexed in the bowtie2 index file, but do not appear in the fasta file. The resolution is that this situation will be detected early during setup.

9 Jan 2013. Fixed several issues involving the detection of pairing information. Removed hard-coding of paths to awk and python. Updated INPUT_PHRED detection.

20 Dec 2012. Various fixes. Notably, the README claimed one can reuse mappings to a real reference to run alu-detect on a fake reference. This was wrong; one must map the read set to the fake reference, too.

14 Dec 2012. We ran alu-detect on 7 WGS datasets, and the resulting calls can be found here. Also included are the calls made on an exome capture dataset for one of the 7 individuals for which we analyzed WGS datasets, and also a list of high-confidence calls that were used to estimate nick site preferences.