Commit 1aaabec6 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed columns

parent d9308ceb
......@@ -116,8 +116,8 @@ At this moment the following variant callers can be used
| shiva | use_analyze_covariates | Boolean | true | Analyze covariates during base recalibration step | all |
| shiva | bam_to_fastq | Boolean | false | Convert bam files to fastq files | Only used when input is a bam file |
| shiva | correct_readgroups | Boolean | false | Attempt to correct read groups | Only used when input is a bam file |
| shiva | amplicon_bed | Path | Path to target bed file | all |
| shiva | regions_of_interest | Array of paths | Array of paths to region of interest (e.g. gene panels) bed files | all |
| shiva | amplicon_bed | Path | | Path to target bed file | all |
| shiva | regions_of_interest | Array of paths | | Array of paths to region of interest (e.g. gene panels) bed files | all |
| vcffilter | min_sample_depth | Integer | 8 | Filter variants with at least x coverage | raw |
| vcffilter | min_alternate_depth | Integer | 2 | Filter variants with at least x depth on the alternate allele | raw |
| vcffilter | min_samples_pass | Integer | 1 | Minimum amount of samples which pass custom filter (requires additional flags) | raw |
......
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