Structural Variation

GASV on Helix/Biowulf

/usr/local/bin/java64 -Xmx8g -jar /data/CCRBioinfo/biowulf/local/src/gasv/bin/BAMToGASV.jar 5_BD13EMACXX.361_BUSTARD-2012-07-05.fq.hg19.bwa.sorted.bam -MAPPING_QUALITY 30 -CUTOFF_LMINLMAX SD=3 -LIBRARY_SEPARATED all

Output from this step looks like this:

-rw-r----- 1 sdavis2 sdavis2  39G Jul 27 15:54 5_BD13EMACXX.361_BUSTARD-2012-07-05.fq.hg19.bwa.sorted.bam
-rw-r--r-- 1 sdavis2 sdavis2 165M Jul 30 12:39 5_BD13EMACXX.361_BUSTARD-2012-07-05.fq.hg19.bwa.sorted.bam_all.deletion
-rw-r--r-- 1 sdavis2 sdavis2 1.1M Jul 30 12:39 5_BD13EMACXX.361_BUSTARD-2012-07-05.fq.hg19.bwa.sorted.bam_all.inversion
-rw-r--r-- 1 sdavis2 sdavis2 192M Jul 30 12:39 5_BD13EMACXX.361_BUSTARD-2012-07-05.fq.hg19.bwa.sorted.bam_all.divergent
-rw-r--r-- 1 sdavis2 sdavis2 2.2M Jul 30 12:39 5_BD13EMACXX.361_BUSTARD-2012-07-05.fq.hg19.bwa.sorted.bam_all.translocation
-rw-r--r-- 1 sdavis2 sdavis2    0 Jul 30 12:39 5_BD13EMACXX.361_BUSTARD-2012-07-05.fq.hg19.bwa.sorted.bam_all.insertion
-rw-r--r-- 1 sdavis2 sdavis2   32 Jul 30 12:39
-rw-r--r-- 1 sdavis2 sdavis2  331 Jul 30 12:39

The next step is to use GASV to cluster and call the SVs:

/usr/local/bin/java64 -Xmx20g -jar /data/CCRBioinfo/biowulf/local/src/gasv/bin/GASV.jar --fast --batch


DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

Installed in /data/CCRBioinfo/biowulf/local/delly.