# List of scripts in the directory:
Also see https://github.com/tjleez/popgen.methods

## Read quality summary
fastqc.sh

## Reads trimming
trimmmomatic.sh

## Read mapping, sort, mark duplicates
bwa.sh
samtools.depth

## BCFtools mpileup
mpileup.sh

## BCFtools caller
bcfcall.sh

## FreeBayes variant calling
submit_freebayes_batch.sh

## variant filtering
variant_filter.sh
 
## get intersection of variant site from both caller
bcftools isec -p vcf_intersect v10.1.vcf.gz v13.3.vcf.gz

## phylogeny
iqtree_create_phylip_NARL.sh
iqtree_MFP_NARL.sh
iqtree_ASC_NARL.sh

## Admixture
admix0.sh
admix1.sh

## TreeMix
treemix.k29.sh

## consensus sequence fasta per isolate
bcfconsensus.sh     #print ambiguous code
bcfconsensus.v3.sh  #print first allele

## print multiple sequence fasta from vcf
vcf2fa.py

## VariScan
variscan.run2.sh
vs.output.sh

## count pairwise differences between isolates from input.vcf.fa
pairdiv_vcf.fa.py

## cout pairwise differences between isolates from a list of fasta files
pairdiv_fa.list.py

## retrieve CDS sequence from full length fasta
getCDS.sh

## create multiple sequence fasta of each gene, for isolates within a lineage
mergeCDS.sh

## translate from CDS, providing BED file
translate.from.bed.py

## dN/dS
pal2nal.sh
run.codeml.sh
parse.out.sh

## rho estimate
subset.vcf.sh
rhomap.sh
get.mean.rho.sh

## MK test
popgenome.R

