Dindel

From UFRC
Jump to navigation Jump to search

Description

dindel website  

Dindel is a program for calling small indels from short-read sequence data ('next generation sequence data'). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls.

See Dindel 1.01 Manual (PDF) for more details.

Required Modules

modules documentation

Serial

  • dindel

System Variables

  • HPC_DINDEL_DIR - installation directory
  • HPC_DINDEL_DOC - documentation directory (PDF manual)

How To Run

The following executables are available:

  • dindel - main binary
  • Utilities: convertVCFToDindel.py makeGenotypeLikelihoodFilePooled.py makeWindows.py mergeOutputDiploid.py mergeOutputPooled.py selectCandidates.py





Validation

  • Validated 4/5/2018