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PGGSVpipeline

PGGSVpipeline version 2.0, 20220826.

  • Program: PGGSVpipeline (Population Genomics Group Structural Variation calling pipeline)
  • Contact: Yimin Wang [email protected]
Usage:     PGGSVpipeline.sh -b <input.bam> -i <sampleSID> 
           -s <software_list> -r <reference_genome> -f <ref.fasta>

Required parameters:

           -b   the mapped sequences in bam format
           -r   choose a build-in reference genome (hg19/hg38/chm13)
        or
           -f   use a user reference genome

Optional parameters:

           -i   task SID
           -s   enter a comma-separated list of software. 'all' is equal to 'breakdancer,breakseq2,cnvnator,lumpy,manta,metasv'
                please note that breakseq2 can only be used with hg19 or hg38 (default all)

Please replace the path in the parameter.sh file in the script directory with your own path. We recommend using conda to install:

breakdancer

breakseq2

cnvnator

lumpy

manta

metasv

to avoid errors due to conflicting dependent environments.