Difference between revisions of "VarDictJava"

From UFRC
Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
Line 39: Line 39:
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 +
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Revision as of 20:01, 27 May 2022

Description

vardictjava website  

VarDictJava is a variant discovery program written in Java and Perl. It is a partial Java port of VarDict variant caller.

The original Perl VarDict is a sensitive variant caller for both single and paired sample variant calling from BAM files. VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads and better scalability than Java based variant callers.

Required Modules

Serial

  • gcc/5.2.0
  • vardictjava

System Variables

  • HPC_VARDICTJAVA_DIR - installation directory
  • HPC_VARDICTJAVA_BIN - executable directory




Citation

If you publish research that uses vardictjava you have to cite it as follows:

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research