# README

This repository contains genotype data generated and analyzed in the manuscript
"Positive selection plays a major role in shaping signatures of differentiation
across the genomic landscape of two independent Ficedula flycatcher species pairs"

# Genotype data

coll.pied.par.taig.hyp.SNPs.minDP.maxDP.minGQ.RM.auto_scaffs.vcf.gz

This file contains SNP calls generated with GATK HaplotypeCaller followed by
GenotypeGVCFs for collared, pied, red-breasted and taiga flycatchers, as well
as the outgroup Ficedula hyperythra. Hard filter thresholds have been applied
to the data (QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0),
and SNPs falling within annotated repeats are removed. 9 pied and 7 taiga samples
with high amounts of missing data have been removed.Genotype filters for minimum
depth of 5, maximum depth 200 and minimum genotypequality 30 have been applied,
however sites with high amounts of missing data have not yet been removed from
this file. Only scaffolds mapping to autosomesaccording to the collared flycatcher
reference genome are included.

# Missing data

Missing data was removed for each analysis for the species included. The following
files contain sites found to have greater than 10% missing data for each species
or pair of species. For species pairs, sites with greater than 10% missing data
in either species were removed.

## Missing in collared
missing_sites_coll_max_10_perc_auto.txt.gz

## Missing in pied
missing_sites_pied_max_10_perc_auto.txt.gz

## Missing in red-breasted
missing_sites_par_max_10_perc_auto.txt.gz

## Missing in taiga
missing_sites_taig_max_10_perc_auto.txt.gz

## Missing in collared and pied
missing_sites_coll_pied_max_10_perc_auto.txt.gz

## Missing in collared and red-brested
missing_sites_coll_par_max_10_perc_auto.txt.gz

## Missing in collared and taiga
missing_sites_coll_taig_max_10_perc_auto.txt.gz

## Missing in pied and red-breasted
missing_sites_pied_par_max_miss_10_perc_auto.txt.gz

## Missing in pied and taiga
missing_sites_pied_taig_max_miss_10_perc_auto.txt.gz

## Missing in red-breasted and taiga
missing_sites_par_taig_max_10_perc_auto.txt.gz

# Species information

pop_file.txt

This file contains a list of samples included in the VCF file
and the species that each sample corresponds to.

Coll = collared
Par = Red-breasted
Taig = Taiga

# Collapsed regions

collapsed_regions.bed

This file contains the regions that were identified as putatively collapsed
duplicates in the assembly. SNPs falling within these regions were removed from
all analyses.