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-- these are the scripts used to make the SomaticSniper VCFs from the bamfiles -- they were run on stampede
- gtdownload : this is the script used to download the TCGA bamfiles from cghub
- bam_to_fastq.sh : this is the script used to run picard to convert bamfiles to fastqs
- align_fastq.sh : this is the script used to align the re-generated fastqs to hg19 using bwa
- SNPs_GATK.sh : this is the script used to run GATK base recalibration and indel alignmnet
- SNPcalling.sh : this is the script used to run SomaticSniper on all samples/home1/01839/dakotaz/GBM_genomics/MAKE_VCF
#################
#################
-- 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
#################
#################
-- These are the scripts that were used to filter the VCFs -- they were run on phylocluster
##############
##############
-- these are the custom python scripts used to analyze the VCF data -- they were run on phylocluster
- compare_overlap_to_filtered.py :
- compare_size_of_overlap.py :
- double_compare_number_mutations.py :
- filtered_by_filter.py :
- germline_snps.py :
- how_many_muts.py :
- overlap_by_chrom.py :
- overlap_only_filter_by_filter.py :
- overlap.py :
- sort_doubles.py :
- VCF_list.py :
#############
#############
-- these are the custom scripts, run in R, used to make the figures in the paper -- they were run on a Macbook
-- there are
-- These are the scripts (or other documents) used to produce the figures in FIGURE_PDFS
- Figure1.key is the keynote document that is Figure 1
- Figures.R is the R script used to make figures 2-8, and also to do statistical calculations
-- figures for the paper are in .pdf form and are numbered 1-8
###########
###########
-- 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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-- 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
- BigData2015.key is the poster in Keynote
- BigData2015.pages is the text only
- BigData2015.pdf is the pdf for printing