SoftClippedReadFilter

Filter out reads that are over-soft-clipped

Category Read Filters

Overview

Filter out reads where the ratio of soft-clipped bases to total bases exceeds some given value. Can choose to filter by number of soft-clipped bases, or by the leading/trailing soft-clipped bases only.

SoftClippedReadFilter 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 Tool Arguments
--max-soft-clipped-leading-trailing-ratio		Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases in read for read to be filtered.
--max-soft-clipped-ratio		Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in read for read to be filtered.

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.

--max-soft-clipped-leading-trailing-ratio

Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases in read for read to be filtered.

Exclusion: This argument cannot be used at the same time as max-soft-clipped-ratio.

Double null

--max-soft-clipped-ratio

Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in read for read to be filtered.

Exclusion: This argument cannot be used at the same time as max-soft-clipped-leading-trailing-ratio.

Double null

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.