diff --git a/README.md b/README.md index f89db8261851fa36fa67a3362fc7c85f208a680e..1ae564e4a7a400edf3d326a1eeb144c9dd58cf02 100644 --- a/README.md +++ b/README.md @@ -53,6 +53,7 @@ The `bamcalib` expect the following parameters: - `-c`, `--cal-prefix <cal_prefix>` calibration prefix added to the chromosome name of the calibration genome (default: `calib_`) - `-h`, `--help` Print help information +- `-s`, `--scaling <SCALING>` multiply the OR by this value (must be the same across sample) [default: 1000] - `-n`, `--no_bits <no_bits>` remove reads which bit code match this code. You can use [this site](https://broadinstitute.github.io/picard/explain-flags.html) to get an appropriate bit code. The default is `1540` for - segment unmapped - not passing quality controls