analysis of low coverage heteroclitus and grandis genome resequencing data

many analyses are run using "parallel" on the UConn HPC cluster.

directory 'align':

grandis_align.sh - base script that aligns and sorts individual Fundulus grandis samples
het_align.sh - base script that aligns and sorts individual Fundulus heteroclitus samples
$POP_align.slurm - these files invoke *_align.sh using 'parallel' for each population. submitted to slurm job scheduler
other scripts compress and sort split and discordant read files

directory 'genome_stats':

basecomp.slurm - calculates base composition in windows for reference genome
$POP_cov.slurm - calculates coverage in windows for each population or species
grandis_subpops_cov.slurm - loops through all grandis populations to calculate coverage

directory 'variants':

call_variants_subregion.sh - basic variant calling script. invoked using parallel
directory 'chunks':
- 300 scripts which each invoke call_variants_subregion.sh on a set of regions adding up to approximately 3.4mb