ESR-NZ/vcf_annotation_pipeline ESR-NZ/vcf_annotation_pipeline

  • Stars
    star
    8
  • Rank 2,099,232 (Top 42 %)
  • Language
    Python
  • Created over 4 years ago
  • Updated over 2 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
ESR-NZ/vcf_annotation_pipeline
github

ESR-NZ

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

A Snakemake workflow to filter, annotate and prepare variant call format (VCF) data for scout using GATK4, SnpSift, VEP and genmod. Designed to be used after human_genomics_pipeline.

More Repositories

1

human_genomics_pipeline

A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
Python
30
star
2

covid_in_wastewater

Quantitative data about how much SARS-CoV2 virus is found in New Zealand's wastewater
19
star
3

NZ_COVID19_Data

13
star
4

nz-sars-cov2-variants

Data on prevalence of variants of concern in Aotearoa New Zealand
11
star
5

NZ_SARS-CoV-2_genomics

Shell
6
star
6

POx_POC_pipeline

Point of care species ID by kraken2 ONT read classification for Xaiver platform
Python
5
star
7

GraphPanGenomes_Microbial

Microbial genomics pipeline to build and analyse genome graphs
Roff
3
star
8

Training

training materials
2
star
9

Notifiable-Diseases-Annual-Dashboard-

This repository is to make Annual Notifiable Disease Dashboard data public.
2
star
10

2019-05-28-DC-ESR-MASC

MASC DC Workshop 28-29 May 2019
Python
2
star
11

2020-11-24-ESRpython

HTML
1
star
12

GenomicsNarrativeSARSCoV2

A companion document to the genomics data from NZ cases
1
star
13

human_genomics_pipeline_gpu

A GPU accelerated Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using bwa/GATK4.
Python
1
star