I'm trying to recalibrate some bams using the following:
gatk --java-options "-Xmx8g" ApplyBQSR -I $insampleID.sorted.dups.bam \ -R $reference --bqsr-recal-file $outsampleID.table \ -O $outsampleID.recal.bam
Every time I try, I get the following error:
A USER ERROR has occurred: Argument output was missing: Argument 'output' is required.
The following, within the same script, was used to successfully produce the table I needed for the above, and its output is the same as the non-functional output above, except with a different extension.
gatk --java-options "-Xmx8g" BaseRecalibrator \ -I $insampleID.sorted.dups.bam \ -R $reference --known-sites $recal \ -O $outsampleID.table
(I know that in the ApplyBQSR block, the first line is missing a \ - if I try to include it, I instead get an error saying my argument, ' ' was invalid....)
Can anyone help me out? I've reformatted it a hundred times, tried making an empty output bam in the destination folder, and I know others have used the script I'm running successfully in the past.
Same error sadly