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/>.
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@@ -8,23 +10,69 @@ For mapping details please look into the original publication ([Harr et al. 2016
## 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_: