Amaranthus population genomics

This repository contains sets of pipelines for various population genomic analyses of a diploid, dioecious plant with a reference assembly:

1. Alignment and bam processing - Preprocess FASTQ's, run BWAmem, process bams with sambamba, picard to GATK
2. SNP calling and filtering - Call SNPs with freebayes and filter
3. PLINK pipelines and related analyses - Running PLINK, treemix, faststructure, & beagle
4. Getting basic summary stats (Dxy, Fst, Pi, ABBA-BABA) - Use genomicsgeneral scripts from Simon Martin
5. Estimating recombination rates - Use LDhat and Hapcut to estimate Rho
6. Detecting selective sweeps - selscan, H12, & sweepscan2
7. Investigating introgression - Run hapmix on phased samples
8. Investigating copy number - Custom R scripts for plotting coverage per individual and by region to investigate copy number heterogeneity
9. De novo assembly - Using spades