Minimum weight parameter for lumpy.

Absolute path to reference.fa. Should have reference.dict and .fai files in the same directory

Require that SVs be reported as the same type of event from different callers. Used by SURVIVOR

Name of genome, eg: hg19. Should match snpEff db

Require that SVs be reported on the same strand from different callers. Used by SURVIVOR

Array of bam files. Contains cfDNA/plasma samples. Should have .bai files in same directory

snpEff db. Example: /location/of/database/hg19

Minimum required number of total split-reads + paired-end reads that support a variant.

Tab-delimited bed file of SV hotspots. Each line in the bed file should describe a likely breakpoint region. For example, if one end of a suspect structural variant is expected to be around chr1:5000, the bed file might include 'chr1 4000 6000'.

Bed file. Neither end of SV should fall in these regions

Bed file. Max of one end of SV is allowed to be in these regions

Bed file of target regions from targeted sequencing

Minimum bp length to be considered. Used by SURVIVOR

Minimum number of callers that must call an SV for it to be considered a consensus call. Range 1-3.

Array of bam files. Should be in the same order as sample_bams (ie the nth sample in each array are matches). Should have .bai files in same directory

Array of bams used as an unmatched, panel of normals. Should have accompanying .bai files

Parameter for SURVIVOR - merging distance of SVs