split_by_allele C>T SNPs at CpG sites

[rnbatra]

Thank you for including the split_by_allele tutorial. Would this work suitably for C>T SNPs at CpG sites as well (using reads on the opposite strand for directional libraries)?

[yonniejon]

Hi. Yes. For C->T SNPs both at CpG sites and outside of CpG sites split_by_allele considers only reads from the opposite/bottom strand. Similarly it considers only reads from the top strand for G->A SNPs.

This information will be added to the tutorial/documentation.

[rnbatra]

thanks for the clarification!