Changes

Set these values.  If you used a different path for any of these, please update here.  Also, be sure to specify your sample name instead of Sample_XXXXX

Set these values.  If you used a different path for any of these, please update here.  Also, be sure to specify your sample name instead of Sample_XXXXX

  source /home/mktrost/seqshop-server/setup.txt

  source /home/mktrost/seqshop/setup.txt

  export SAMPLE=Sample_XXXXX

  export SAMPLE=Sample_XXXXX

Verify that this does not give an error:

Verify that this does not give an error:

  ls $OUT/bams/${SAMPLE}.recal.bam

  ls $OUT/bams/${SAMPLE}.recal.bam

== Run ==

== Run ==