Giter VIP home page Giter VIP logo

broad-fungalgroup's Introduction

broad-fungalgroup

Broad Fungal Genomics group scripts

This repository hosts scripts used publications to carry out fungal genomic analyses.

Genotype filtering (filterGatkGenotypes.py)

Usage example:

filterGatkGenotypes.py --min_GQ 50 --min_percent_alt_in_AD 0.8 --min_total_DP 10 ${VCF} > ${FILTERED_VCF} 2> variant_qc_genotype_filter.tsv

create whole genome fasta-alignment from VCF (SNPs only) (vcfSnpsToFasta.py)

Usage example:

python vcfSnpsToFasta.py --max_amb_samples 40 list_vcf > filtered.SNPs.fa

create gene fasta-alignment from VCF (SNPs only) (vcfSnpsToGeneFasta.py)

Usage example:

python vcfSnpsToGeneFasta.py list_of_vcf_files reference.fasta reference.gff gene_id > output.fasta

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.