Out of curiosity, I compared the two different SNP-inputs of WASP. To my big surprise, it seems that using the --snp_dir in find_intersecting_snps.py results in more discarded and bad reads compared to HDF5. I read that there are some expected differences due to phasing information: is this what I see here? And if so, could you maybe elaborate on this?
Hi there,
Out of curiosity, I compared the two different SNP-inputs of WASP. To my big surprise, it seems that using the
--snp_dirinfind_intersecting_snps.pyresults in more discarded and bad reads compared to HDF5. I read that there are some expected differences due to phasing information: is this what I see here? And if so, could you maybe elaborate on this?Thanks, Robin