Commit 9bfac77b authored by bow's avatar bow
Browse files

Merge branch 'patch-doc_fixes' into 'develop'

Patch doc fixes

Part of the docs in develop are still in there old setup. Should be added to dev.

See merge request !86
parents 8be170d4 7e7e2526
......@@ -72,16 +72,16 @@ Global setting examples are:
#### Example settings config
~~~
{
"reference": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/ucsc.hg19_nohap.fasta",
"dbsnp": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
"reference": "/references/hg19_nohap/ucsc.hg19_nohap.fasta",
"dbsnp": "/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
"joint_variantcalling": false,
"haplotypecaller": { "scattercount": 100 },
"multisample": { "haplotypecaller": { "scattercount": 1000 } },
"picard": { "validationstringency": "LENIENT" },
"library_variantcalling_temp": true,
"target_bed_temp": "/data/LGTC/projects/vandoorn-melanoma/analysis/target.bed",
"target_bed_temp": "analysis/target.bed",
"min_dp": 5,
"bedtools": {"exe":"/share/isilon/system/local/BEDtools/bedtools-2.17.0/bin/bedtools"},
"bedtools": {"exe":"/BEDtools/bedtools-2.17.0/bin/bedtools"},
"bam_to_fastq": true,
"baserecalibrator": { "memory_limit": 8, "vmem":"16G" },
"samtofastq": {"memory_limit": 8, "vmem": "16G"},
......@@ -95,4 +95,4 @@ Global setting examples are:
### JSON validation
To check if the JSON file created is correct we can use multiple options the simplest way is using [this](http://jsonformatter.curiousconcept.com/)
website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
\ No newline at end of file
website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
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