DELLY

DELLY: Structural variant discovery by integrated paired-end and split-read analysis

홈페이지 : http://www.embl.de/~rausch/delly.html

다운로드 : https://github.com/tobiasrausch/delly

### Set environment

$ export BOOST_ROOT=/BiO/apps/boost_1_53_0/

$ export BAMTOOLS_ROOT=/BiO/apps/bamtools-master/

$ export SEQTK_ROOT=/BiO/apps/seqtk

$ export LD_LIBRARY_PATH=/BiO/apps/bamtools-master/bamtools/lib

### install delly

$ make -B src/delly

$ ./delly 

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DELLY Copyright (C) 2012-2014 Tobias Rausch

This is free software, and you are welcome to redistribute it under

certain conditions (GPL); for license details use '-l'.

This program comes with ABSOLUTELY NO WARRANTY; for details use '-w'.

DELLY (Version: 0.5.4)

Contact: Tobias Rausch (rausch@embl.de)

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Usage: ./delly [OPTIONS] <sample1.sort.bam> <sample2.sort.bam> ...

Generic options:

  -? [ --help ]                    show help message

  -t [ --type ] arg (=DEL)         SV analysis type (DEL, DUP, INV, TRA)

  -o [ --outfile ] arg (="sv.vcf") SV output file

  -x [ --exclude ] arg (="")       file with chr to exclude

PE options:

  -q [ --map-qual ] arg (=0)   min. paired-end mapping quality

  -s [ --mad-cutoff ] arg (=5) insert size cutoff, median+s*MAD (deletions 

                               only)

SR options:

  -g [ --genome ] arg          genome fasta file

  -m [ --min-flank ] arg (=13) minimum flanking sequence size

Genotyping options:

  -v [ --vcfgeno ] arg (="site.vcf") input vcf file for genotyping only

  -u [ --geno-qual ] arg (=20)       min. mapping quality for genotyping