Changes between Initial Version and Version 1 of net.sf.basedb.reggie/notes413


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Timestamp:
Nov 13, 2017, 11:53:38 AM (5 years ago)
Author:
Nicklas Nordborg
Comment:

Create update notes for Reggie 4.13

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  • net.sf.basedb.reggie/notes413

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     1= Updating to Reggie 4.13 =
     2
     3=== Genotyping with HaplotypeCaller in the Hisat pipeline ===
     4
     5In `reggie-config.xml` the following changes are required:
     6
     7 * In the `<programs>` section, a `<java>` sub-section should be added with the full `<path>` to a Java executable. It must be at least Java 8 since GATK will not work with earlier versions.
     8
     9 * In the `<programs>` section, a `<gatk>` sub-section should be added with the full `<path>` to the Genome Analysis Toolkit JAR file (https://software.broadinstitute.org/gatk/download/).
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     11 * In the `<align-hisat>` section, three new configuration options need to be added:
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     13  - `<haplotypecaller-ref>`: Path to FASTA file used to create the reference that Hisat is aligning against
     14  - `<haplotypecaller-dbsnp>`: Path to a VCF file with SNP definitions that we are looking for
     15  - `<haplotypecaller-options>`: Other static options for the !HaploypeCaller
     16
     17Note that all paths are relative the `<reference-dir>` directory.