Input(s)

One sample : lumpy search structural variations inside a single sequencing dataset

Two samples: lumpy search structural variations inside and across two sequencing datasets from two samples

Analysis of sample replicates is not implemented yet in this wrapper

BAM files: Only BAM alignments produced by BWA-mem have been tested with this tool

Sequencing method

Paired-end sequencing: Both ends of library fragments have been sequenced, resulting in two paired sequencing datasets

Single-read sequencing: Only one end of library fragment has been sequenced, resulting in a single sequencing dataset. Under these conditions, evidences of structural variation are obtained only from splited read alignments

Read length: The length of the sequencing reads in the library. This information is required only for paired-end sequencing data

Additional options: refer to lumpy-sv documentation and the publication (doi 10.1186/gb-2014-15-6-r84)

lumpy-sv manual

Read the lumpy-sv documentation for details on using lumpy.

lumpy options

v 0.2.13 Author: Ryan Layer (rl6sf@virginia.edu)

Summary: Find structural variations in various signals.

Options:

-g      Genome file (defines chromosome order)
-e      Show evidence for each call
-w      File read windows size (default 1000000)
-mw     minimum weight for a call
-msw    minimum per-sample weight for a call
-tt     trim threshold
-x      exclude file bed file
-t      temp file prefix, must be to a writeable directory
-P      output probability curve for each variant
-b      output BEDPE instead of VCF
-sr     bam_file:<file name>,
        id:<sample name>,
        back_distance:<distance>,
        min_mapping_threshold:<mapping quality>,
        weight:<sample weight>,
        min_clip:<minimum clip length>,
        read_group:<string>

-pe     bam_file:<file name>,
        id:<sample name>,
        histo_file:<file name>,
        mean:<value>,
        stdev:<value>,
        read_length:<length>,
        min_non_overlap:<length>,
        discordant_z:<z value>,
        back_distance:<distance>,
        min_mapping_threshold:<mapping quality>,
        weight:<sample weight>,
        read_group:<string>

-bedpe  bedpe_file:<bedpe file>,
        id:<sample name>,
        weight:<sample weight>