ExcessiveEndClippedReadFilter

Filter out reads that have too many clipped bases on either end.

Category Read Filters

Overview

Filter out reads where the number of soft-/hard-clipped bases on either end is above a certain threshold. This filter will filter reads where the number of soft clips on one end of the read is too large. It does NOT check the total number of bases clipped on BOTH ends. For the purposes of this filter, the count of soft and hard clipped bases on either end of a read are combined. For example, a read with the following cigar strings will be filtered out (given maxClippedBases=1000): 1500S0000M 900H300S50000M 1001H50000M However, this read will NOT be filtered out (given maxClippedBases=1000): 900S50000M900S 150H800S50000M900S150H 1000S500M 500M1000S Note: This is designed for use with (unpaired) long reads, but can be used with any reads.

ExcessiveEndClippedReadFilter 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-clipped-bases	1000	Maximum number of clipped bases on either end of a given read

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-clipped-bases

Maximum number of clipped bases on either end of a given read

int 1000 [ [ -∞ ∞ ] ]

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