Variant Calling
Variant calling is the process by which we identify variants (such as SNPs, insertions or deletions) from sequence data. This data, which is stored in a VCF file, can be used to annotate variants, if you are interested in the genetic and coding consequences of each mutation, and to associate variants to phenotypic traits, in order to know if a variant is significantly related to a characteristic. There are different algorithms specifically designed to achieve this goal:
- BCFtools: this is a widely-used variant calling tool, especially among non-human species, which is characterized by its small time of execution and its precision.
- Freebayes: this tool is characterized by its capability to use it with polyploid genomes.
OmicsBox Engine
This tool can be run from the command line via the OmicsBox Engine.
Command: omicsbox variantcalling-multipackage [options]
Inputs
| Flag | Type | Required | Description |
|---|---|---|---|
--i-input-files |
file (multiple) | Yes | BAM Files |
--i-ref-gen |
file | Yes | Reference Genome |
--i-group-experiment |
file | No | Group Experiment File |
Parameters
| Flag | Type | Default | Range / Candidates | Required | Description |
|---|---|---|---|---|---|
--remove-duplicates |
boolean | true | No | Remove Duplicates | |
--adj-mp |
integer | 0 | ≥ 0 | No | Adjust Mapping Quality |
--max-dp |
integer | 250 | ≥ 0 | No | Max. Depth |
--baq |
enum | -B | -B-E-D |
No | BAQ options |
--min-mq |
integer | 0 | ≥ 0 | No | Min. Mapping Quality |
--min-bq |
integer | 13 | ≥ 0 | No | Min. Base Quality |
--ignore-rg |
boolean | false | No | Ignore @RG Tags | |
--ext-prob |
integer | 20 | ≥ 0 | No | Extension Error Probability |
--gap-frac |
double | 0.002 | ≥ 0.0 | No | Minimum Fraction of Gapped Reads |
--tand-qual |
integer | 500 | ≥ 0 | No | Tandem Quality |
--skip-indel |
boolean | false | No | Skip Indel Calling | |
--min-ireads |
integer | 1 | ≥ 1 | No | Gapped Reads for Indel |
--open-prob |
integer | 40 | ≥ 0 | No | Phred Open Sequencing Error |
--keep-alts |
boolean | true | No | Keep Alternate Alleles | |
--use-groups |
boolean | false | No | Use Groups | |
--chart-format |
enum | box | boxpngpdfcsv |
No |
Parameter relationships
| Flag | When | Effect | Affected flags |
|---|---|---|---|
--use-groups |
true |
enables | --i-group-experiment |
Global options (
--local-folder,--cloud-folder,--output-format,--config,--detach,--verbose, …) are shared by every Engine tool and are not repeated here — see the OmicsBox Engine reference.