complete addition of beauty annotation module, mostly to merge_sample.sh

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@4556 8f329c14-d232-4f17-8684-7ee34322b8dc
complete addition of beauty annotation module, mostly to merge_sample.sh [forgot to add]

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@4557 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@4707 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@4758 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@4965 8f329c14-d232-4f17-8684-7ee34322b8dc
fixing the issue for beauty samples

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5450 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5508 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5509 8f329c14-d232-4f17-8684-7ee34322b8dc
turn on and off somatic calling when user wants to do multi sample calling

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5691 8f329c14-d232-4f17-8684-7ee34322b8dc
merging the realigned bam with the unaligned reads bam

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5693 8f329c14-d232-4f17-8684-7ee34322b8dc
merging the multi allelic calls to single allele calls in the variant calling scripts

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5705 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5713 8f329c14-d232-4f17-8684-7ee34322b8dc
changing the scripts to make sure it works with the new parameters 

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5800 8f329c14-d232-4f17-8684-7ee34322b8dc
not required 

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5801 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5808 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5815 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5852 8f329c14-d232-4f17-8684-7ee34322b8dc
fixed a bug of extra tab in TSV file

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5859 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5873 8f329c14-d232-4f17-8684-7ee34322b8dc
git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@5874 8f329c14-d232-4f17-8684-7ee34322b8dc