MalformedReadFilter

Filter out malformed reads.

Category Read Filters


Overview


Command-line Arguments

MalformedReadFilter specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Optional Flags
--filter_bases_not_stored
 -filterNoBases
NA if a read has no stored bases (i.e. a '*'), filter out the read instead of blowing up.
--filter_mismatching_base_and_quals
 -filterMBQ
NA if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up.
--filter_reads_with_N_cigar
 -filterRNC
NA filter out reads with CIGAR containing the N operator, instead of stop processing and report an error.

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.


--filter_bases_not_stored / -filterNoBases

if a read has no stored bases (i.e. a '*'), filter out the read instead of blowing up.

boolean


--filter_mismatching_base_and_quals / -filterMBQ

if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up.

boolean


--filter_reads_with_N_cigar / -filterRNC

filter out reads with CIGAR containing the N operator, instead of stop processing and report an error.

boolean


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GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA