Deleting useless file
gmap.patch: patch to make gsnap output both SAM & natural format (-A sam)

mutect_pair.py: wrapper to run muTect for the given (tumor, normal) pair

paired_mutect.py: procedure to run muTect for prim/recur/normal triples specified in the input file
- added 'igv.log' for ignored file list

gsnap2sam.py: [WIP] backing up source to convert gsnap output to sam format

mygsnap.py: modified and added several functions to accommodate sam format conversion
- not used currently. For future use by gsnap2sam.py

split_gsnap_sam.py: separating gsnap's merged output into natural format (.gsnap) & sam format
prepDB_cosmic.py:
modified regular expression to handle indel

prepDB_cosmic_annotated.py: prepare cosmic DB & VEP annotation (/data1/Sequence/cosmic/cosmic_annotated_v**.dat)
- joining with this table will attach all VEP annotations for confirmed somatic mutation in cosmic
- cosmic_annotated.sql : sql script for the db ('cosmic_a')
util/link_bam.py : make links with standarized names for .recal.bam