Commit 5e274379 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Update some content

parent f3ebafca
......@@ -89,6 +89,7 @@ At this moment the following variant callers can be used
* <a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_genotyper_UnifiedGenotyper.php">unifiedgenotyper_allele</a>
* Only genotype a given list of alleles with UnifiedGenotyper
* <a href="https://samtools.github.io/bcftools/bcftools.html">bcftools</a>
* <a href="https://samtools.github.io/bcftools/bcftools.html">bcftools_singlesample</a>
* <a href="https://github.com/ekg/freebayes">freebayes</a>
* [raw](../tools/MpileupToVcf)
......@@ -108,6 +109,8 @@ To view all possible config options please navigate to our Gitlab wiki page
| Namespace | Name | Type | Default | Function |
| ----------- | ---- | ----- | ------- | -------- |
| shiva | species | String | unknown_species | Name of species, like H.sapiens |
| shiva | reference_name | String | unknown_reference_name | Name of reference, like hg19 |
| shiva | reference_fasta | String | | reference to align to |
| shiva | dbsnp | String | | vcf file of dbsnp records |
| shiva | variantcallers | List[String] | | variantcaller to use, see list |
......@@ -122,7 +125,6 @@ To view all possible config options please navigate to our Gitlab wiki page
| vcffilter | min_alternate_depth | Integer | 2 | Filter variants with at least x depth on the alternate allele |
| vcffilter | min_samples_pass | Integer | 1 | Minimum amount of samples which pass custom filter (requires additional flags) |
| vcffilter | filter_ref_calls | Boolean | true | Remove reference calls |
| vcfstats | reference | String | Path to reference to be used by `vcfstats` |
Since Shiva uses the [Mapping](mapping.md) pipeline internally, mapping config values can be specified as well.
For all the options, please see the corresponding documentation for the mapping pipeline.
......@@ -151,26 +153,23 @@ The config for these therefore is:
**Config example**
```json
{
"samples": {
"SampleID": {
"libraries": {
"lib_id_1": { "bam": "YourBam.bam" },
"lib_id_2": { "R1": "file_R1.fq.gz", "R2": "file_R2.fq.gz" }
}
}
},
"shiva": {
"reference": "<location of fasta of reference>",
"variantcallers": [ "haplotypecaller", "unifiedgenotyper" ],
"dbsnp": "</path/to/dbsnp.vcf>",
"vcffilter": {
"min_alternate_depth": 1
}
},
"output_dir": "<output directory>"
}
``` yaml
samples:
SampleID:
libraries:
lib_id_1:
bam: YourBam.bam
lib_id_2:
R1: file_R1.fq.gz
R2: file_R2.fq.gz
dbsnp: <dbsnp.vcf.gz>
vcffilter:
min_alternate_depth: 1
output_dir: <output directory>
variantcallers:
- haplotypecaller
- unifiedgenotyper
- haplotypecaller_gvcf
```
## References
......
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