GATK4 ApplyBQSRSpark VS PrintReadsSpark

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created by mgujral

on 2017-05-01

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

From Sheila on 2017-05-04

@mgujral

Hi Madhu,

I just moved your question to the GATK4 forum where someone else will help.

Sheila

From mgujral on 2017-05-08

Thanks Sheila

From LouisB on 2017-05-15

@mgujral You should use ApplyBQSRSpark if you want to apply BQSR recalibration to a bam file using spark.

Both PrintReadsSpark and ApplyBQSRSpark output a bam file, but only ApplyBQSRSpark performs the recalibration.