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Filter out reads that were generated by a specific sequencing platform

Category Read Filters


This filter is useful for running on only a subset of the data as identified by a read group property. In the case of the platform filter, the goal is usually to blacklist certain sequencing technologies at certain processing steps if we know there is an incompatibility problem (like 454 and indel realignment, which is special-cased).

Usage example

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf Platform \
         -PLFilterName platform_name

Command-line Arguments

PlatformFilter 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
NA Discard reads with RG:PL attribute containing this string

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.

--PLFilterName / -PLFilterName

Discard reads with RG:PL attribute containing this string

String[]  NA

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.