Difference: MikSeminarsVariantBiasExercises (1 vs. 11)

Revision 11
09 Jan 2013 - Main.PerryMoerland
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META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

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Variant selection and accounting for data bias

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  • The links provided below can be used during the computer exercises.

Data

Revision 10
07 Jan 2013 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 11 to 11
 

Variant selection and accounting for data bias

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  • The links provided below can be used during the computer exercises.
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  • See yesterday's exercises for the instructions of how to work with the VirtualBox and the virtual machine and disk
 

Data

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  • ANNOVAR file (Excel) with annotated variants for all four Nicolaides-Baraitser patients

SARA HPC Cloud: software

Note: instructions for installation are provided below only in case you want to install these tools on your own computer. All tools that are required for the computer exercises are pre-installed in the SARA HPC Cloud. An IP number, login name and password will be provided to you.

UNIX

 

R

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  • To install a package see instructions
  • Note: R and the required packages are already pre-installed in the provided VirtualBox.
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Tools

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  • BWA (Burrows-Wheeler Aligner)
    • Manual
    • bz2 file can be unzipped with 'bunzip2 file '
    • tar file can be extracted with tar -xvf file
    • compile code with 'make -f Makefile'
    • download chromosome 9 (fasta file) from the UCSC database
    • Note: BWA and the reference sequence for chromosome 9 are already pre-installed in the SARA HPC Cloud.

  • VarScan
    • Documentation
    • make sure to set the program as an executable: chmod a+x
    • Start program from command line with 'java -jar VarScan.v2.2.jar'
    • Use the program 'java -jar VarScan.v2.2.jar pileup2cns'
    • Note: VarScan is already pre-installed in the SARA HPC Cloud.
 

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    • Note: AnnoVar is already pre-installed in the provided VirtualBox.

Genomes

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    • Note: AnnoVar is already pre-installed in the SARA HPC Cloud.
 
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  • SAMtools
    • use bunzip2, tar -xvf and make -f Mafefile to install samtools
    • Note: SamTools is already pre-installed in the SARA HPC Cloud.
 
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-- PerryMoerland - 2012-01-24
  \ No newline at end of file
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Revision 9
07 Jan 2013 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

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BackSort
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BackSort
 

Revision 8
17 Sep 2012 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 22 to 22
 
  • Coverage data for the TEQC pacakge. Download and then load in R.

R

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  • Page on our course Statistical Computing in R with lots of useful material and links
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  • Page on our course Statistical Computing in R with lots of useful material and links
 
Revision 7
25 Jan 2012 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 19 to 19
 
Added:
>
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  • Coverage data for the TEQC pacakge. Download and then load in R.
 

R

  • Page on our course Statistical Computing in R with lots of useful material and links
Revision 6
25 Jan 2012 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 11 to 11
 

Variant selection and accounting for data bias

Changed:
<
<
>
>
 
  • The links provided below can be used during the computer exercises.
  • See yesterday's exercises for the instructions of how to work with the VirtualBox and the virtual machine and disk
Revision 5
25 Jan 2012 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 36 to 36
 
Deleted:
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Data formats

 

Genomes

Revision 4
25 Jan 2012 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 17 to 17
 

Data

  • ANNOVAR file (tab-delimited) with annotated variants for all four Nicolaides-Baraitser patients
Added:
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  • bam file of the Nicolaides-Baraitser exome experiment
 

R

Revision 3
24 Jan 2012 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 19 to 19
 
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R tutorial

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R

  • Page on our course Statistical Computing in R with lots of useful material and links
 
Revision 2
24 Jan 2012 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 16 to 16
 
  • See yesterday's exercises for the instructions of how to work with the VirtualBox and the virtual machine and disk

Data

Added:
>
>
  • ANNOVAR file (tab-delimited) with annotated variants for all four Nicolaides-Baraitser patients
 

R tutorial

 
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