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 |
null | 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 |
null | 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 / NA
Inverts the results from this filter, causing all variants that would pass to fail and visa-versa.
boolean false
--soft-clipped-leading-trailing-ratio / NA
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 / NA
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 4.1.4.1 built at Thu, 5 Dec 2019 09:51:56 -0500.
3 comments
Hi there,
I have a question: Is this function already available? Can you please provide an example line code and required arguments please
Same here I'm afraid.
I pulled v4.2.0.0 as a docker, but cannot see this command available?
An example usage would also be greatly appreciated!
Bump for the last two requests for an example
edit: providing the link to this article from all relevant "filter" commands would be nice. Additionally, a place to easily view a list of all these available filters, preferably also linked from the haplotypecaller docs underneath where it specifies the default filters, would be nice
https://gatk.broadinstitute.org/hc/en-us/articles/360035532092-Read-filters
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