Data Prep and Read QC

Before starting, make sure that the following variables are defined in your shell environment. That means, you will need to type the following when you launch a new shell terminal:

MYBASE=/home/mtb_upm/mapping-variantcalling
MYDATA=$MYBASE/data
MYRESULTS=$MYBASE/results

Create a separate directory for the .vcf files:

mkdir $MYRESULTS/vcf