SNP calling for one chromosome using mpileup

[zhanglu295]

I tried to use mpileup in samtools to call SNP and indel from 200 individuals of whole genome sequencing. However, it is a time consuming job, in about 10 days, only the variants in three chromosomes have been outputted in the bcf file. So, if the mpileup can make variants call separately in chromosomes, I can run multiple chromosomes at the same time on my computer. But the parameter -l need the user to provide candidate variants position.Does anyone have some experence in this situation?

[gaffa]

I think you can supply regions in BED format to the -l flag, so then you could put down whole chromosomes as your regions.