# Scripts for the Publication:

Ullrich KK, Tautz D

## Data sources

Genome mapping files for _Mus musculus domesticus GER_, _Mus musculus domesticus FRA_, _Mus musculus domesticus IRA_, _Mus musculus musculus AFG_, _Mus musculus castaneus CAS_ and _Mus spretus SPRE_ were obtained from <http://wwwuser.gwdg.de/~evolbio/evolgen/wildmouse/m_m_domesticus/genomes_bam/>, <http://wwwuser.gwdg.de/~evolbio/evolgen/wildmouse/m_m_musculus/genomes_bam/>, <http://wwwuser.gwdg.de/~evolbio/evolgen/wildmouse/m_m_castaneus/genomes_bam/>, <http://wwwuser.gwdg.de/~evolbio/evolgen/wildmouse/m_spretus/genomes_bam/>.

For mapping details please look into the original publication ([Harr et al. 2016](http://www.nature.com/articles/sdata201675)) <http://www.nature.com/article-assets/npg/sdata/2016/sdata201675/extref/sdata201675-s7.docx>.

## Get masking regions for individual samples and natural populations

For masking genomic regions in natural populations which showed low coverage based on the genomic mapping BAM files we only considered the stable chromosomes from the reference GRCm38 _mm10_ <http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/>.

The BAM files were processed with 'genomeCoverageBed' to obtain site specific genome coverage and further united with 'unionBedGraphs'. The per population combined coverage was further processed to only retain regions with a coverage smaller than 5 resulting as the masking regions.

genomeCoverageBed example for the population _Mus musculus musculus AFG_:
```
#example for populaton Mmm_AFG:
#
#used BAM files:
#
#AFG1_396.bam
#AFG2_413.bam
#AFG3_416.bam
#AFG4_424.bam
#AFG5_435.bam
#AFG6_444.bam

$REFERENCE=mm10.fasta

for file in *.bam; do genomeCoverageBed -ibam $file -bga -g $REFFERENCE > $file".bga";done
```

unionBedGraphs example for the population _Mus musculus musculus AFG_:
```
INPUT1=AFG1_396.bam.bga
INPUT2=AFG2_413.bam.bga
INPUT3=AFG3_416.bam.bga
INPUT4=AFG4_424.bam.bga
INPUT5=AFG5_435.bam.bga
INPUT6=AFG6_444.bam.bga

OUTPUT=Mmm_AFG.combined.bga

unionBedGraphs -i $INPUT1 $INPUT2 $INPUT3 $INPUT4 $INPUT5 $INPUT6 | awk -v OFS='\t' 'BEGIN {sum=0} {for (i=4: i<=NF; i++) sum+=$1; print $1,$2,$3,sum; sum=0}' > $OUTPUT
```

get masking region example for the population _Mus musculus musculus AFG_:
```
INPUT=Mmm_AFG.combined.bga
OUTPUT=Mmm_AFG.combined.bga.stcov5
awk '{if($4<5) print $0}' $INPUT > $INPUT".stcov5"
bedtools merge -i $INPUT".stcov5" > $INPUT".stcov5.merge"
awk -v OFS='\t' '{print $1,$2,$3,4}' $INPUT".stcov5.merge" > $OUTPUT
```

_used software:_

+ bedtools v2.24.0 <http://bedtools.readthedocs.io/en/latest/>
+ awk

## SNP and INDEL calling

_used software:_

## K80 distance calculation

### Get population specific SNPs

_used software:_

### Calculate population specific Consensus sequence

_used software:_

### Calculate K80 distance between populations

## Dxy distance calculation

### Calculate Dxy distance between populations

_used software:_

### Calculate Dxy distance between individuals and populations

_used software:_