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

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

4 ()

fasta (file)

Optional - reference FASTA file needed when the input is a CRAM file

*.{fasta,fa}

fasta_fai (file)

Optional - index of the reference FASTA file needed when the input is a CRAM file

*.fai

dict (file)

Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file

*.dict

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

gatk4 Documentation

Genome Analysis Toolkit (GATK4)

https://github.com/broadinstitute/gatkdoi: 10.1158/1538-7445.AM2017-3590License: BSD-3-clause
Authors