Part 1. Manta Structural Variants Identification
Manta
This step executes the manta.sh script, which runs the Manta algorithm to identify potential structural variations (SVs) in the input data.
The output is a vcf file, which is then checked for integrity to confirm that the format is correct and the file is complete.
- CWL: workflow_manta_integrity-check.cwl
Input
The script takes analysis-ready bam file(s), generated from either of the CGAP Upstream modules.
The input file(s) can also be provided directly by the user.
Running Manta
Manta executes a Joint Diploid Sample Analysis when more than one sample is provided, and a Single Diploid Sample Analysis when run for a single sample (i.e., proband-only).
The algorithm identifies deletions (SVTYPE=DEL), duplications (SVTYPE=DUP), insertions (SVTYPE=INS), and inversion/translocations (SVTYPE=BND).
A callRegions region file containing a list of chromosome names limits the search to canonical and sex chromosomes (i.e., chr1-chr22, chrX and chrY).
The script convertInversion.py (https://github.com/Illumina/manta) is also run to separate (SVTYPE=INV) from other translocations (SVTYPE=BND).