OverclippedReadFilter

Filter out reads that are over-soft-clipped

Category Read Filters


Overview

This filter is intended to filter out reads that are potentially from foreign organisms. From experience with sequencing of human DNA we have found cases of contamination by bacterial organisms; the symptoms of such contamination are a class of reads with only a small number of aligned bases and additionally many soft-clipped bases. This filter is intended to remove such reads. Consecutive soft-clipped blocks are treated as a single block


Command-line Arguments

OverclippedReadFilter 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 Parameters
--filter_is_too_short_value
 -filterTooShort
30 Value for which reads with less than this number of aligned bases is considered too short
Optional Flags
--do_not_require_softclips_both_ends
 -NoRequireSCBothEnds
false Allow a read to be filtered out based on having only 1 soft-clipped block. By default, both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped block.

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.


--do_not_require_softclips_both_ends / -NoRequireSCBothEnds

Allow a read to be filtered out based on having only 1 soft-clipped block. By default, both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped block.

Boolean  false


--filter_is_too_short_value / -filterTooShort

Value for which reads with less than this number of aligned bases is considered too short

int  30  [ [ -∞  ∞ ] ]


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GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.