Currently:
/sample/Script/coverage.sh is called to fire up
/nfs/chgv/seqpipe01/SOFTWARE/alignment_scripts/average_coverage.pl
$script_dir/average_coverage.pl $pileup_file > $coverage_file
Now,
Step 1. Copy “average_coverage.pl” to lsrc svnroot
Step 2. Modify “average_coverage.pl” to take in vcf format
Step 3.