mitool refine-tags

Correct tag sequences

Usage:

mitool refine-tags [OPTIONS] SOURCE DESTINATION

Arguments:

SOURCE

Input *.mic file

DESTINATION: Output *.mic file.

Options:

-t, --tag <TEXT>

Name(s) of the tags to correct, each subsequent tag is corrected inside the group of equal tags going before it in the list. To correct a tag against a fixed set add a set specification separated by a hash sign after the tag name, i.e. "CELL#preset:737K-august-2016" or "UMI#file:my_umi_list.txt". !!! note if --preset was used on the parse step you most probably can run this command without additional parameters as the appropriate defaults will be set for you from the preset collection

-p, --power <FLOAT> (default: 0.001 or from preset)

This parameter determines how thorough the procedure should eliminate variants looking like errors. Smaller value leave less erroneous variants at the cost of accidentally correcting true variants. This value approximates the fraction of erroneous variants the algorithm will miss (type II errors).

-s, --substitution-rate <FLOAT> (default: 0.001 or from preset)

Expected background non-sequencing-related substitution rate

-i, --indel-rate <FLOAT> (default: 1.0E-5 or from preset)

Expected background non-sequencing-related indel rate

-q, --min-quality <INT> (default: 12 or from preset)

Minimal quality score for the tag. Tags having positions with lower quality score will be discarded, if not corrected.

--max-substitutions <INT> (default: 2 or from preset)

Maximal number of substitutions to search for.

--max-indels <INT>(default: 2 or from preset)

Maximal number of indels to search for.

--max-errors <INT> (default: 3 or from preset)

Maximal number of indels and substitutions combined to search for.

--use-system-temp

Use system temp folder for temporary files

-r, --report <PATH>

Human readable report file. If file already exists, it will be overwritten.

-h, --help: Show this message and exit