Converts a GEM-mappability file into a BED-graph format

Description

Converts a GEM-mappability ( Derrien et al. 2012) file into a BED-graph format.

The GEM-mappability format is a FASTA-like file with:

  • Header including information for the algorithm applied (e.g., k-mer size).
  • Sequences in FASTA-like format: sequence name preceded by ~ and a character per-base encoded in the header. Each character encodes a different range of values, which represent the number of mappings of the reads starting at that position.

This tool parses the GEM-mappability file and outputs a per-position BED-graph format. For each position, different scoring systems could be use (see arguments for more information).

Arguments

Required Arguments

Argument name(s) Type Description
--input
-I
String GEM-mappability file (FASTA-like) to parse
--output
-O
String Bed-graph output with the number of mappings as score. If it contains a block-compressed extension (e.g., .bgz), it will be compressed.

Optional Arguments

Argument name(s) Type Default value(s) Description
--arguments_file List[File] [] read one or more arguments files and add them to the command line
--gcs_max_retries
-gcs_retries
int 20 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--help
-h
boolean false display the help message
--score-method GemScoreMethod MID Method to convert number of mappings within a range into the reported score

Possible values: MIN (Minimum of the range of mappings.), MAX (Maximum of the range of mappings.), MID (Middle point of the range of mappings.)
--version boolean false display the version number for this tool

Optional Common Arguments

Argument name(s) Type Default value(s) Description
--forceOverwrite
-forceOverwrite
Boolean false Force output overwriting if it exists
--QUIET Boolean false Whether to suppress job-summary info on System.err.
--TMP_DIR List[File] [] Undocumented option
--use_jdk_deflater
-jdk_deflater
boolean false Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use_jdk_inflater
-jdk_inflater
boolean false Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity
-verbosity
LogLevel INFO Control verbosity of logging.

Possible values: ERROR, WARNING, INFO, DEBUG

Advanced Arguments

Argument name(s) Type Default value(s) Description
--showHidden
-showHidden
boolean false display hidden arguments