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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


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