Can chromap deal with haplotypes

[zhangzhiyangcs]

Hi, I want compared the difference between two haplotypes. Can chromap directly alignment two haplotypes? If I want to get alignmet files of two haplotypes precisely. How to get it?

[mourisl]

Do you mean to align reads to the two haplotypes simultaneously? Like concatenate the two genomes and then run Chromap? I think in this case, most of the reads will have MAPQ 0 since it can be aligned to two places, and may cause some confusion between real repeats or just the homologous region between haplotypes.

If you are aligning on two haplotypes independently with separate indices, I think it is fine. Note that the default output from Chromap is in BED, which does not contain read id. If you want to compare the reads whose alignment coordinate changed (and MAPQ>0 separately), you might want to specify other output formats in Chromap, such as --PAF, --SAM.

[zhangzhiyangcs]

Thanks a lot, I will try.