Medizinische Genomanalysen 2017 - Assignment 3

dependencies:

vcf-tools: https://vcftools.github.io/perl_module.html

sudo python install_vcftools.py

Overview

• Fork and clone the repository
• Complete the python program, based on the template, to calculate various properties
• Push to your repository

Attention!

As the HGVS package does only support Python2, please run the script with Python2

Data

• Son
  • HG002-NA24385-huAA53E0
  • ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/IonTorrent_TVC_03162015/AmpliseqExome.20141120.NA24385.vcf
• Mother
  • HG004-NA24143-hu8E87A9
  • ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/IonTorrent_TVC_03162015/AmpliseqExome.20141120.NA24143.vcf
• Father
  • HG003-NA24149-hu6E4515
  • ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/IonTorrent_TVC_03162015/AmpliseqExome.20141120.NA24149.vcf

Tools

• hgvs (https://hgvs.readthedocs.io/en/master/) - only works with Python 2
• cyvcf2 (https://github.com/brentp/cyvcf2)