Scripts for initial data processing renameFiles.sh: Rename files in diferent situations Usage: renameFiles.sh bam/fastq pattern/table_file dataset_name createMakefile.sh: create a makefile from a sample-library table to run paleomix Usage: createMakefile.sh dataset_name table_file fastq_path sample_makefile runPaleomix.sh: Run Paleomix for several samples at once and samtools to split them Usage: runPaleomix.sh run_dir makefile dataset_name ref_name threads getPaleomixStats.sh plotPaleomixStats.R getInsertSize.sh runSamtoolsDepth.sh plotSamtoolsDepth.R