Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.


noushinnoushin Member
edited May 2014 in Ask the GATK team

Hello GATK team,

I have a question regarding the PrintReads walker. I am running it with the --BQSR engine using the command below. While my job has yet to finish, it is clear that the output bam file will be significantly larger than the input (~2x). I have not set the –emit_original_quals flag, so I expect that the original scores should be discarded. Should I still be expecting this size increase?

     java -Xmx${heap}m -Djava.io.tmpdir=${temp_folder}/applyRecal_${sample}\
     -jar ${gatk}\
     -T PrintReads\
     -R ${refSequence}\
     -I ${SCRATCH}/${sample}.realigned.bam\
     -BQSR ${SCRATCH}/${sample}.recal_data.table\
     -o ${SCRATCH}/${sample}.recalibrated.bam\
     -nct 4

Thanks so much,


Best Answer


Sign In or Register to comment.