-y is undocumented in the help message. It's also missing in minimap2's help message, but you can still find it in the minimap2 man page. This option has become more relevant as the need to have modified base information (encoded in MM & ML SAM/BAM tags) has grown. These MM/ML tags can be copied as comments (anything after the first whitespace) into the FASTQ header from the uBAM containing reads (e.g., via samtools fastq -T MM,ML). That FASTQ can be used as input to Winnowmap, and -y allows those tags to be added to the output alignment SAM or PAF. Downstream tools (e.g., modkit) can then use those tags to determine the modified base status from the aligned read evidence.
cjain7
commented
5 months ago
-y is undocumented in the help message. It's also missing in minimap2's help message, but you can still find it in the minimap2 man page. This option has become more relevant as the need to have modified base information (encoded in MM & ML SAM/BAM tags) has grown. These MM/ML tags can be copied as comments (anything after the first whitespace) into the FASTQ header from the uBAM containing reads (e.g., via samtools fastq -T MM,ML). That FASTQ can be used as input to Winnowmap, and -y allows those tags to be added to the output alignment SAM or PAF. Downstream tools (e.g., modkit) can then use those tags to determine the modified base status from the aligned read evidence.