For SNP and INDEL calling the BAM files were processed with 'samtools mpileup' and 'bcftools call' with relaxed quality options to retain information in CNV regions.
Due to the amount of data first mpileup files were generated for each BAM file and merged with 'bcftools merge'. After merging mpileup files, 'bcftools call' was used to generate the final VCF file.
samtools mpileup | bcftools call example for the population _Mus musculus musculus AFG_:
```
#example for population Mmm_AFG:
#
#used BAM files:
#
#AFG1_396.bam
#AFG2_413.bam
#AFG3_416.bam
#AFG4_424.bam
#AFG5_435.bam
#AFG6_444.bam
#generating indiviual mpileup files for each BAM file