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BME 383J Course Content

Your Instructors

Name

Initials

Affiliation

Expertise

Scott Hunicke-Smith

SPHS

Director GSAF

Everything, if loosely defined (but especially awk)

John Fonner

JF

Research Associate, TACC Life Sciences

high performance computing

Matt Vaughn

MWV

Manager, TACC Life Sciences

in absentia

Jeff Barrick

 

Asst. Prof. Biochemistry

in absentia

Tuesday Nov. 6th

 Homework - expand this section for the assignment
  1. Log in to Lonestar via ssh
  2. Copy data files that will be required for Thursday's homework:
    1. Define a BASH variable to the genomics data repository at TACC like this:
      How to define the variable BI in a bash shell
      BI="/corral-repl/utexas/BioITeam"
      

Thursday Nov. 8th

 Homework - expand this section for the assignment

Go to this web page and call variants from real human genomes from the 1000 genomes project.
Helpful hint: start this early - it involves some long run times at TACC.
IMPORTANT NOTE: you must use "-a BME2012" with the launcher_creator.py command.

Tuesday Nov. 13th

  • Review NGS - from cellular DNA to variant data
  • Review results of variant calling - for these examples, Start IGV, load the genome, "Human (1kg, b37+)", load the three NA*.bam files (the corresponding *.bai must exist in the same directory).
    Command to view the contents of a sorted (by genome coordinates) BAM file
    samtools view NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | head
    
    Examine the first read of the file which matches at genome position chr20:59993
    • Examine a pileup in text and in IGV
      Command to generate a "pileup" - data oriented in "genome coordinates" by genome base-pair
      samtools mpileup -f ref/hs37d5.fa NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | more
      
      Examine the area around chr20:60614
    • Examine a variant in text and in IGV
      Command to call variants
      samtools mpileup -uf ref/hs37d5.fa NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | bcftools view -vcg - | more
      
      - look at the SNP at base 76771
      Examine the SNP at chr20:76771
  • SNP Annotation
  • Reference databases (if time permits)
  • No labels