SVPipeline

Available tools¶

All the programs are available on the genotoul plateform

• BreakDancer http://breakdancer.sourceforge.net
  • supported SV : DEL, INV
  • No reference genome needed
  • Works in multiple sample mode
  • Necessary insert sizes are computed by the script bam2cfg.pl
  • Parallelization can be obtained at the chromosome level using -o

• CNVnator https://github.com/abyzovlab/CNVnator
  • supported SV : DEL, DUP
  • No specific index file for the reference genome
  • Works in multiple sample mode
  • a list of chromosomes must be provided
  • chromosomes are specified using the -chrom option
  • No multi-threading mode (mentionned)
  • Need to Select a bin size, see CNVnatorbinsize

• Delly https://github.com/tobiasrausch/delly
  • supported SV : DEL, INV, DUP
  • No specific index files for the reference genome
  • Works on different SV type independantly
  • Works in multiple sample mode
  • Works in multi-threading mode by setting OMP_NUM_THREADS (#threads <= #samples)
  • Single chromosome run is not implemented
  • uses paired-ends and split-reads to detect SV

• Lumpy https://github.com/arq5x/lumpy-sv
  • supported SV : DEL, INV, DUP, BND
  • No reference genome needed
  • Works in multiple sample mode
  • The bam file needs to be split in 3 bam files : full, discordants and splitters
  • Single chromosome run is not implemented
  • No multi-threading mode (mentionned)
  • svtyper is used to genotype the individuals

• Pindel http://gmt.genome.wustl.edu/packages/pindel
  • supported SV : DEL, INV, DUP, INS
  • No specific index file for the reference genome
  • Works in multiple sample mode
  • Estimated insert size has to be given in a config file
  • Single chromosome run is implemented using the -c option
  • Works in multi-threading mode -T option

• GenomeStrip http://software.broadinstitute.org/software/genomestrip
  • supported SV : DEL, multi-copy CNV
  • A reference bundle has to be created

Encoding structural variants in vcf¶

see
http://www.internationalgenome.org/wiki/Analysis/Variant%20Call%20Format/VCF%20(Variant%20Call%20Format)%20version%204.0/encoding-structural-variants/

The pipeline software¶

1. Preliminary step for genomeSTRIP
   ReferenceBundel
2. The software

• Delly https://github.com/tobiasrausch/delly
• Lumpy https://github.com/arq5x/lumpy-sv
• Pindel http://gmt.genome.wustl.edu/packages/pindel
• GenomeStrip http://software.broadinstitute.org/software/genomestrip

The process is next divided in 6 different steps

1. prepare
   compute library parameters and RD statistics
   • cnvnatorStats for read depth statistics
   • breakdancerStats for insert size statistics
   • bamstats for insert size statistics
   • results in the stats dir, on directoty for each animal
   • TODO : a summary table with the statistics for each individual
2. preprocess
   preprocess the data for genomeSTRIP, see
   http://software.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_SVPreprocess.html
   • results in genomestrip/metada dir
3. run
   Run the SV detection pipeline for a list of software
   • results in each tool specific dir
4. parse
   Parse the SV tool output files and write corresponding vcf files
   • Parse is donne for a given sv type (DEL for the moment)
   • TODO: add parse for DUP and INV
5. merge
   Merge the SV for
6. genotype
   Genotype a set of sv given in a vcf file
   • genotyping is donne with genomestrip
   • limited to DEL for the moment
7. filter
   Select a set of SV based on genotype qualities, redundancy, variation status,....

Good practice for filtering SV calls :
SVFiltering

The jflow pipeline
JflowPipeline¶

The simulations
JflowSimulations¶