Lumpy-sv is a software for finding and categorizing structural variation in genome sequencing data
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
[user@helix]$ module avail lumpy-sv ----------------------------- /usr/local/Modules/3.2.9/modulefiles -------------------------- lumpy-sv/0.1(default)
[user@helix]$ module load lumpy-sv [user@helix]$ module list Currently Loaded Modulefiles: 1) lumpy-sv/0.1 [user@helix]$ module unload lumpy-sv [user@helix]$ module load lumpy-sv/0.1 [user@helix]$ module list Currently Loaded Modulefiles: 1) lumpy-sv/0.1
Sample Session 1
The following example workflow is from the documentation link at the end of this page.
Assuming that the input files are"hg19.fa", "sample.1.fq" and "sample.2.fq" and arelocated under /data/$USER/lumpy-sv, and the read length is 150:
$ cd /data/$USER/lumpy-sv
$ module load lumpy-sv
$ bwa aln hg19.fa sample.1.fq > sample.1.sai
$
bwa aln hg19.fa sample.2.fq > sample.2.sai
$ bwa sampe hg19.fa sample.1.sai sample.2.sai sample.1.fq sample.2.fq | samtools view -S -b - > sample.pe.bam
$
samtools view sample.pe.bam | split_unmapped_to_fasta.pl -b 20 > sample.um.fq
$
bwa bwasw -H sample.um.fq | samtools view -Sb - > sample.sr.bam
$ samtools view sample.pe.bam | pairend_distro.pl -rl 150 -X 4 -N 10000 -o sample.pe.histo
# pairend_distro.pl will display mean and stdev to screen, we will assume the mean=500 and stdev=50
$ lumpy -mw 4 -tt 1e-3 -pe bam_file:\
sample.pe.bam,histo_file:sample.pe.histo,mean:500,stdev:50,read_length:150,min_non_overlap:150,\
discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1 > sample.pe.bedpe
$ lumpy -mw 4 -tt 1e-3 -sr bam_file:\
sample.sr.bam,back_distance:20,weight:1,id:1,min_mapping_threshold:1 > sample.sr.bedpe
$ lumpy -mw 4 -tt 1e-3 -pe bam_file:\
sample.pe.bam,histo_file:sample.pe.histo,mean:500,stdev:50,read_length:150,min_non_overlap:150,\
discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1 -sr bam_file:sample.sr.bam,\
back_distance:20,weight:1,id:1,min_mapping_threshold:1 > sample.pesr.bedpe
Sample Session 2
A test directory and data which came with lumpy-sv package can be copied from /usr/local/apps/lumpy-sv/
Resulting output files will be generated in /data/$USER/lumpy-sv/data
$ mkdir /data/$USER/lumpy-sv
$ cd /data/$USER/lumpy-sv
$ cp /usr/local/apps/lumpy-sv/data.tar.gz .
$ tar xvfz data.tar.gz
$ cp -r /usr/local/apps/lumpy-sv/test ./test
$ module load lumpy-sv
$
cd /data/$USER/lumpy-sv/test
$ ./test.sh
