Changes between Version 1 and Version 2 of net.sf.basedb.reggie/notes413


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Timestamp:
Nov 23, 2017, 8:27:30 AM (7 years ago)
Author:
Nicklas Nordborg
Comment:

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  • net.sf.basedb.reggie/notes413

    v1 v2  
    11= Updating to Reggie 4.13 =
    22
    3 === Genotyping with HaplotypeCaller in the Hisat pipeline ===
     3=== Genotyping with !HaplotypeCaller in the Hisat pipeline ===
    44
    5 In `reggie-config.xml` the following changes are required:
     5In `reggie-config.xml` the following changes are required (included in the default configuration that is shipped with Reggie):
    66
    77 * 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.
    … …  
    1010
    1111 * In the `<align-hisat>` section, three new configuration options need to be added:
    12 
    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 
    17 Note that all paths are relative the `<reference-dir>` directory.
     12  - `<haplotypecaller-ref>`: Path to FASTA file used to create the reference that Hisat is aligning against.
     13  - `<haplotypecaller-dbsnp>`: Path to a VCF file with SNP definitions that we are looking for.
     14  - `<haplotypecaller-options>`: Other static options for the !HaploypeCaller.
     15 Note that the paths are relative the `<reference-dir>` directory.