domvie/medizinische_genomanalysen_2019_assignment_2

Medizinische Genomanalysen 2019 - Assignment 2

Medizinische Genomanalysen 2019 - Assignment 2

Overview

• Fork and clone the repository
• Complete the python program, based on the template, to calculate various properties
• Complete all TODOs
• Hint: Call the individual methods from print_summary
• Commit (often)
• Push to your repository

Data

• VCF chr21: http://hmd.ait.ac.at/medgen2019/chr21.vcf
• VCF chr22: http://hmd.ait.ac.at/medgen2019/chr22.vcf
• All datasets http://hmd.ait.ac.at/medgen2019/

Data backup

• VCF chr21: http://hmd.ait.ac.at/medgen2019/chr21_new.vcf
• VCF chr22: http://hmd.ait.ac.at/medgen2019/chr22_new.vcf

Tools

• pyvcf (http://pyvcf.readthedocs.io/en/latest/)

Work

• Perform the calculation using chr22
• Only when implementing the method merge_chrs_into_one_vcf use both chromosomes (chr21 and chr22)