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- Mapped read data evaluation (SAMtools)
- Installing Linux tools
- Identifying mutations in microbial genomes (breseq)
- Genome variation in mixed populations
- Practical advice - short read re-sequencing data
- Calling variants in diploid genomes
- Structural variation
- SRA toolkit, UCSC Genome Browser
- 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
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- Resources: tool list, file formats & more
- Scott's list of linux one-liners
- Example BWA alignment script\
- Exercises
Misc
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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.
Daechan original|../../../../../../../../../display/bioiteam/Daechan+original\ shell scripting page