cutevariant

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Create a Pedigree Chart

3

Probably related to #101. By reading the documentation of SnpEff & SnpSift: https://pcingola.github.io/SnpEff/examples/ By the way, **I strongly recommend writing such a tutorial before any new implementation of anything; it...

ysard

All history is display in Edit Only concerned history must be displayed

antonylebechec

[samples view] create a source from samples without existing filters on "filters view"

1

Because creating source from samples is mostly used to select all variants for these samples, but without any other filters. To create a source from samples with existing filters, it's...

antonylebechec

Add a plugin to show history, by modified table

antonylebechec

Add an "Open Config" item in Cutevariant menu "File" to open another config file. The idea is to switch between configuration, and especially presets, to create a exploration/validation context

antonylebechec

Create history table to track changes in validation fields

antonylebechec

In order to homogenize validation fields in tables - table "samples" ``` valid INTEGER DEFAULT 0, tags TEXT DEFAULT '', comment TEXT DEFAULT '', ``` - table "sample_has_variant" ``` {...

antonylebechec

A plugin to check miss-validated variants: - "Variants already validated in some samples but not all of them" ``` SELECT distinct(variant_id) FROM sample_has_variant WHERE sample_has_variant.classification IN (2) AND sample_has_variant.gt >=1...

antonylebechec

[VCF import] importing vcf with sample already exist clear classification

1

When a VCF is imported and contains a sample that already exists in the project, classification of the sample is set to default value (0, unlock)

antonylebechec

[Import file] Importing VCF with variant-sample already existing

1

When importing a VCF which include an existing variant and sample association, fields count_var, count_het... are recalculated by incrementing number, which is not correct. Test by creating a db with...

antonylebechec