...
- Mapped read data evaluation (SAMtools)
- Installing and compiling tools on Unix
- Integrated pipeline for microbial genome re-sequencing analysis (breseq)
- Calling variants in mixed populations
- Calling variants in diploid or multiploid genomes
- Practical advice about some things to watch out for with short read re-sequencing data
- Calling variants in diploid genomes
- UCSC genome browser, SRA data downloads - 30 min - Anna
- Variant calling with GATK (use their wiki), more detail on .vcf format, look at Human data 1000 genome VCF files and describe how to access 1000 genome data Anna Scott
- Annotating variants annovar/snpeff/plink/vaast/qiime Dhivya & Scott shell/perl/python scripting – candidates for recessive disease
...
Notes from 5/17/12:
Conventions decided on - expands for hints, formats for command prompt/code
Aaron to write .sge maker script
All qsub's will run "./commands"
All examples have to have a "commands" file.
AB/DC to tacc-ify scripts; SPHS to put up chr20 fastq's, bams, and vcf's for example.
Append GATK to diploid calling.