** [http://statgen.us/files/2015/02/francioli/handouts/06-VCF_and_IGV.pdf NGS variants output and visualizaion: VCF and IGV]
* Exercises
** [http://statgen.us/files/2015012015/02/francioli/handouts/01_variant_calling_exercices.pdf Variant calling exercises]** [http://statgen.us/files/2015012015/02/exercises/francioli.tar.bz2 Download Data Sets] (decompress using "tar jxvf francioli.tar.bz2")
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* [http://statgen.us/files/201501/francioli/handouts.tar.bz2 tarball download]
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====Suzanne Leal====
* Presentations
** [http://statgen.us/files/2015012015/02/leal/lectureshandouts/analysis_rare_variants.pdf Complex Trait Associaton Analysis of Rare Variants Obtained from Sequence Data]** [http://statgen.us/files/2015012015/02/leal/lectureshandouts/data_quality_control_2_5_15.pptx Data Quality Control]** [http://statgen.us/files/2015012015/02/leal/lectureshandouts/power_analysis_2_5_15.pdf Sample Size and Power Analysis For Associaton Studies Analysis of Individual Variants]** [http://statgen.us/files/2015012015/02/leal/lectureshandouts/power_analysis_rare_variants_2_5_15.pdf Power Analysis for Rare Variants - Aggregate Analysis]
* Exercises
** [http://statgen.us/files/2015/02/leal/exercises/Armitage_sample_size_Rockefeller_1_5_15.pdf Sample Size Calculation]
** [http://statgen.us/files/2015/02/leal/exercises/SEQPower-2015NYC.pdf SEQPower]
** [http://statgen.us/files/2015/02/leal/exercises/VAT-2015NYC.pdf Variant Association Tools]
** [http://statgen.us/files/2015/02/leal/exercises/leal.tar.bz2 Download Data Sets] (decompress using "tar jxvf leal.tar.bz2")
====Ben Neale====
* Presentations
** [http://statgen.us/files/2015012015/02/neale/handouts/Neale_Rockefeller_course_2015.pdf Neale lectures combined]
* Exercises
** [http://statgen.us/files/2015012015/02/neale/exercises/neale.tar.bz2 Download Data Sets] (decompress using "tar jxvf neale.tar.bz2")
====Shamil Sunyaev====
* Presentations
** [http://statgen.us/files/2015012015/02/sunyaev/handouts/Rockefeller_pop_gen_2014.pdf Population genetics]** [http://statgen.us/files/2015012015/02/sunyaev/handouts/Rockefeller_mutation_2015.pdf Mutation]** [http://statgen.us/files/2015012015/02/sunyaev/handouts/Rockefeller_complex_traits_2015.pdf Complex traits]
* Exercises
** [http://statgen.us/files/2015012015/02/sunyaev/handouts/Rockefeller_tutorial.pdf Annotation tutorial]
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===Data-sets Used During the Course===
* [http://statgen.us/files/2015012015/02/cordell/exercises/cordell.tar.bz2 Heather Cordell's Data Sets]* [http://statgen.us/files/2015012015/02/francioli/exercises/francioli.tar.bz2 Laurent Francioli's Data Sets]* [http://statgen.us/files/2015012015/02/leal/exercises/leal.tar.bz2 Suzanne Leal's Data Sets]* [http://statgen.us/files/2015012015/02/neale/exercises/neale.tar.bz2 Ben Neale's Data Sets]
In order to obtain a particular data set, please follow the following steps:
# Change to this subdirectory (''cd'' command) and proceed with the exercise.
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===Software===
* [http://annovar.openbioinformatics.org/en/latest/ ANNOVAR]