Could you please clarify how exactly:
--max-depth and --high-depth options now (v0.6.4) work in modkit pileup?
In the documentations for 0.6.4 in section Migrating to Modkit v0.6.0+ pileup states:
"--max-depth removed. Modkit v0.6.0 has a new algorithm that doesn’t use max-depth. If you have a modBAM with very high depth and you don’t want to tabulate counts for this depth it is currently recommended to subsample the modBAM before using Modkit."
Since v0.6.4 has "--max-depth", does the "new algorithm" apply only to v0.6.0?
"In Modkit versions v0.6.0 and v0.6.1 pileup will saturate depth at 65,535 (maximum for a unsigned 16-bit integer). If your modBAM has a depth greater than this value, it is recommended to use the --high-depth flag so that 65,535 reads will be used at each genomic position."
Does it mean that the coverage is hard-set to "65,535" if --high-depth is used? And which has precedence if --high-depth and --max-depth are used concurrently?
Thank you for clarification
Marek
Could you please clarify how exactly:
--max-depthand--high-depthoptions now (v0.6.4) work in modkit pileup?In the documentations for 0.6.4 in section
Migrating to Modkit v0.6.0+ pileupstates:Since v0.6.4 has "--max-depth", does the "new algorithm" apply only to v0.6.0?
Does it mean that the coverage is hard-set to "65,535" if --high-depth is used? And which has precedence if --high-depth and --max-depth are used concurrently?
Thank you for clarification
Marek