How to input covariate table to GATK4-Alpha Print Reads

AmandaChamberlainAmandaChamberlain Agriculture VictoriaMember

I'm trying to run PrintReads in GATK4-Alpha and apply the BaseRecalibrator covariates table. Using

java -Xmx80G -jar $GATK PrintReads -R umd_3_1_reference_1000_bull_genomes.fa -I GA1442_dedup.bam -O GA1442_dedup_recal.bam -BQSR recal.table

I get the following error

A USER ERROR has occurred: Invalid command line: B is not a recognized option

I've tried -bqsr --BQSR and --bqsr all with errors saying that they are not recognized options.

-BQSR worked in version 3.5 as an option. The --help for PrintReads does not list an option to input a covariates table. Can you please advise on how to do this in GATK4-Alpha


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