Variant analysis workshop

Dataset Info and TODO:

1 Trio for preprocessing
- two extractions... one that is big (all of the data) and one that is small
- small dataset for the line by line code they (50KB region from the bam file that has SNPS/indels)
- check out how many reads/size of two chromosomes as the big extraction (then subset reads if necessary)
All data from VCF files I already have for Plink stuff (just subset chroms)
Find a paper similar to make sure we are covering everything properly
See if there is any more metadata to stay away from cranio questions and genes

Mon:

CLI/R

Cluster

Tue:

Finish CLI/R

something

Lunch Break

Data Reduction

Fastq file discusion
Running HTS (Brad)
HTStream QA/QC MultiQC (Brad)
samtools/bwa
Bam file discussion
IGG examples, variants in IGG
Visualize trio in IGG to identify variant and inheritance

Wed:

Data Reduction

GATK,FreeBayes,DeepVariant

Lunch Break

Data Reduction

VCF file discussion
Comparisons of FreeBayes/GATK/DeepVariant

Thur:

Data Analysis

Plink
Normal association vs TDT

Anthony Talk?

Try to rope him in to more

Exome Talk?

Lunch Break

Data Analysis

Plink
IBD
Annotation with wAnnovar

Fri:

R visualization of data

Manhattan plots

PlinkQC library

Bioinformatics talk

Experimental Design