| | 1 | **Updated description**\\ |
| | 2 | |
| | 3 | Variant calling is started from Hisat alignment. The first step is a "raw" variant calling using mosdepth and !VarDict. The variant calling only depends on the same reference genome that was used for alignment. We save two files (`variants-callable.bed` and `variants-raw.vcg.gz`) from this step and attaches them to the same Hisat alignment. |
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| | 5 | The seconds step is an annotation step and a filtering step. Multiple programs are used to extract and merge data from a lot of external sources (for example dbSnp, Cosmic, Swegene, etc.) This step creates a child rawbioassay item with two more files. An annotated VCF (`variants-annotated.vcf.gz`) that is the same as the raw VCF with added information from the other database, and a filtered VCF (`variants-filtered.vcf`) with the variants that survive filtering. |
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| | 7 | The variants calling wizard can be executed in two modes: raw-only mode will do only the first step and the full mode will do both steps. In full mode, the raw variant calling can be skipped if it has already been done before. |
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| | 9 | |
| | 10 | **Original description**\\ |
| | 11 | |
