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GATK4: ApplyBQSRSpark VS PrintReadsSpark

Hello there,

What is the difference between GATK4 tools ApplyBQSRSpark and PrintReadsSpark?
java -jar GenomeAnalysisTk-4_1.jar PrintReadsSpark -h suggests that output is String as shown below
--output,-O:String uri for the output file: a local file path.

While on the website https://github.com/broadinstitute/gatk output is bam for PrintReadsSpark option as shown below
./gatk-launch PrintReadsSpark -I input.bam -O output.bam

I plan to start testing GATK-4 in coming days. Any thoughts or suggestions will be greatly appreciated.

best
--Madhu

Answers

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