Integrated htslib/vcftools into mergevcf, two new tool_info parameters HTSLIB and USEHTSLIB, also started refactoring the transfer_clean script to check for presence of files in destination directories and abort if found. 

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Updated merge_raw_variants with htslib mergevcf

git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@8476 8f329c14-d232-4f17-8684-7ee34322b8dc
Removed breakdancer (untested)

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using GATK 2.4.9 and made changes to the script to make sure it works

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deleting the scripts not required for workflow

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Fixed delivery bug, added wrapper to tertiary/variants check.

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Edited error messages for non-empty destination directories.

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used in annotation 

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solved the conflict issues

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Removed .filter. extensions from delivered vcf files in create.igv.pl

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Added 	mv $secondary/Reports_per_Sample/*.final.vcf.idx $delivery/Reports_per_Sample/ to transfer index files to delivery.


git-svn-id: https://bsisvn.mayo.edu/main/projects/g/Genome_GPS/trunk@9194 8f329c14-d232-4f17-8684-7ee34322b8dc
Removed .filter. extension from delivered vcf files


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Added initial checkpoint.sh script

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