Medizinische Genomanalysen 2017

Material and information about the lecture "Medizinische Genomanalysen"

Overview

• Fork & clone the repository of each assignment
• Each student is given an individual assignment to work on
• When done, commit and push the results to your github repository
• All assignments need to be completed by 01.04.2017
• Review process takes place from 02.04.2017 01.05.2017
• Each student needs to review all three assignments of two other students
• Send the review reports (2 students, 3 assignments each) latest on 01.05.2017 to
  email: stephan 'dot' pabinger 'at' ait 'dot' ac 'dot' at
  subject: Medizinische Genomanalysen 2017 - Peer Review
  filetype: PDF
  length: 5-10 sentences per assignment
  checks: correct assignment, working code, correct results, documentation

Data and packages for Python assignments

Data

• BAM file: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/alignment/HG00096.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
• VCF file: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/IonTorrent_TVC_03162015/AmpliseqExome.20141120.NA24385.vcf
• VCF file: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/IonTorrent_TVC_03162015/AmpliseqExome.20141120.NA24143.vcf
• VCF file: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/IonTorrent_TVC_03162015/AmpliseqExome.20141120.NA24149.vcf

Packages

• Biopython (http://biopython.org/)
• pybedtools (https://daler.github.io/pybedtools/)
• NCBI (http://biopython.org/DIST/docs/api/Bio.Entrez-module.html)
• pybam (https://github.com/JohnLonginotto/pybam)
• pysam (http://pysam.readthedocs.io/en/latest/usage.html)
• cyvcf2 (https://github.com/brentp/cyvcf2)
• pyvcf (http://pyvcf.readthedocs.io/en/latest/)
• HGVS - does only work with Python2! (https://hgvs.readthedocs.io/en/master/)

Assignment 1

Repository: medizinische_genomanalysen_2017_assignment_1

Assignment 2

Repository: medizinische_genomanalysen_2017_assignment_2

Assignment 3

Repository: medizinische_genomanalysen_2017_assignment_3

Peer Review - students

Student	Reviewed by
Basílio José	Gutsohn, Moser
Beganovic Alma	Brauneis, Basílio
Bindeus Alexander	Beganovic, Tolios
Brauneis Shelley	Tolios, Tomaselli
Buchner Bianca Allegra	Majewski, Juno
Gollobich Martin	Lang, Lehrach
Gutsohn Tamás	Gollobich, Buchner
Juno Claudia	Spielvogel, Brauneis
Lang Priska	Juno, Gutsohn
Lehrach Michael	Buchner, Beganovic
Majewski Anna	Ruge, Lehrach
Moser Josef	Gollobich, Bindeus
Ruge Frank	Basílio, Lang
Spielvogel Clemens	Tomaselli, Ruge
Tolios Alexander	Moser, Majewski
Tomaselli Anna	Bindeus, Spielvogel

Student projects

TODO -> will be online soon