We are starting a project to explore admixture between populations of two species. We have over 40 low coverage genomes (1-5x coverage) (lcg) and a very good reference genome. We have been mapping our lcg one at a time to the reference genome using bwa and Bowtie2 then using samtools and GATK to explore SNPs/Indels etc.
Is it possible to map all of our lcgs to the reference genome in a single run?
We would like to do various sliding window analyses along our reference genome with all lcgs mapped as a single alignment.