Is variant calling done on a per-position basis? I've read recommendations to split the BAM file by chromosomes and parallel call the chromosomes for speed
Could I further segment each chromosome into chunks and do calling on each chunk? For example if I: 1) Split a chromosome into 1MB segments. 2) Parallel variant call each 1MB segment. 3) Concatenate the VCF.
Would the resulting concatenated file be correct? Would I be missing any information that might be shared among sites on the same chromosome that variant callers use?