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 | |||
| --invert-soft-clip-ratio-filter |
false | Inverts the results from this filter, causing all variants that would pass to fail and visa-versa. | |
| --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. | ||
| --soft-clipped-ratio-threshold |
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.
--invert-soft-clip-ratio-filter
Inverts the results from this filter, causing all variants that would pass to fail and visa-versa.
boolean false
--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 soft-clipped-ratio-threshold.
Double null
--soft-clipped-ratio-threshold
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 soft-clipped-leading-trailing-ratio.
Double null
GATK version 4.3.0.0 built at Wed, 12 Oct 2022 21:04:44 -0400.
1 comment
This tool is available internally to be used with GATK haplotype Caller. But I don't see it as an independent tool in GATK tools list. Is it possible to use it independently?
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