tseemann/snippy

Variant's visualization

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#297 opened on Jul 4, 2019

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help wanted

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Description

Hi,

I am using Snippy for studying the variants between two or more isolates. When I check the variants that appear in the vcf file from Snippy in IGV, I do not see those variants in the BAM files. I have realized that the correspondence is better when I compare a greater number of isolates. Could anybody help me?

Thank you very much!!!

Contributor guide

Research direction
Inspect the VCF and BAM files to verify alignment and check Snippy's variant calling parameters.
Tech stack
perl
Domain
cli
Issue type
Bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
Git
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
50