convering pat file to bam file

[mackaay]

Hi, wgbs_tools looks great. I am just wondering how could we convert pat files to bam files back?

[nloyfer]

Hi @mackaay, and thank you.
There is no way to convert a pat file back to bam, since most of the data in the bam file (the DNA sequence, bp quality, exact read start/length etc.) is discarded when a pat file is created.
This allows pat files to be 300x smaller than their corresponding bam files.