Description
Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
Input
Optional - input VCF of SNPs marking loci for site depths, needed for the site depths output
*.vcf.gz
Optional - index of the VCF file, needed for the site depths output
*.tbi
Optional - index of the reference FASTA file needed when the input is a CRAM file
*.fai