GBM_genomics

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MAKE_VCFs

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-- 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

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JOB_SCRIPTS

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-- 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

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PROCESS_VCF

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-- These are the scripts that were used to filter the VCFs -- they were run on phylocluster

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ANALYSIS

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-- 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 :

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FIGURES

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-- 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

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PAPER

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-- these are the files used to generate the paper and tables in the paper -- they were all created and run on a Macbook

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POSTER

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-- 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