https://github.com/clauswilke/gbm_genomics

https://github.com/clauswilke/gbm_genomics

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• Host: GitHub
• URL: https://github.com/clauswilke/gbm_genomics
• Owner: clauswilke
• Created: 2014-04-07T22:44:19.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2015-11-24T17:17:10.000Z (about 9 years ago)
• Last Synced: 2024-10-14T17:29:14.729Z (3 months ago)
• Language: TeX
• Size: 18.3 MB
• Stars: 3
• Watchers: 5
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
GBM_genomics

============

###############

## MAKE_VCFs ##

###############

-- these are the scripts used to make the SomaticSniper VCFs from the bamfiles

-- they were run on stampede

1. gtdownload : this is the script used to download the TCGA bamfiles from cghub

2. bam_to_fastq.sh : this is the script used to run picard to convert bamfiles to fastqs

3. align_fastq.sh : this is the script used to align the re-generated fastqs to hg19 using bwa

4. SNPs_GATK.sh : this is the script used to run GATK base recalibration and indel alignmnet

5. SNPcalling.sh : this is the script used to run SomaticSniper on all samples/home1/01839/dakotaz/GBM_genomics/MAKE_VCF

#################

## JOB_SCRIPTS ##

#################

-- these are the slurm scripts used to submit jobs to stampede

the five scripts that match names to those in MAKE-VCFs are the slurm scripts that run them

-- there is one script used to submit a job on phylocluster

this script runs scripts from PROCESS_VCF

#################

## PROCESS_VCF ##

#################

-- These are the scripts that were used to filter the VCFs

-- they were run on phylocluster

##############

## ANALYSIS ##

##############

        

-- these are the custom python scripts used to analyze the VCF data

-- they were run on phylocluster

1. compare_overlap_to_filtered.py : 

2. compare_size_of_overlap.py :

3. double_compare_number_mutations.py : 

4. filtered_by_filter.py : 

5. germline_snps.py : 

6. how_many_muts.py : 

7. overlap_by_chrom.py : 

8. overlap_only_filter_by_filter.py : 

9. overlap.py : 

10. sort_doubles.py : 

11. VCF_list.py : 

#############

## FIGURES ##

#############

-- these are the custom scripts, run in R, used to make the figures in the paper

-- they were run on a Macbook

## FIGURE_DATA ##

-- there are 

## FIGURE_SCRIPTS ##

-- These are the scripts (or other documents) used to produce the figures in FIGURE_PDFS

1. Figure1.key is the keynote document that is Figure 1

2. Figures.R is the R script used to make figures 2-8, and also to do statistical calculations

## FIGURE_PDFS ## 

-- figures for the paper are in .pdf form and are numbered 1-8

###########

## PAPER ##

###########

-- these are the files used to generate the paper and tables in the paper

-- they were all created and run on a Macbook

############

## POSTER ##

############

-- these are the files used to generate a poster on this work presented at the Big Data in Biology symposium

-- they were all created and run on a Macbook

1. BigData2015.key is the poster in Keynote

2. BigData2015.pages is the text only

3. BigData2015.pdf is the pdf for printing