# # DDIG: Detecting DIsease-causing Genetic variations # due to indels, nonsense, and synonymous variants # # SUPPORTED FORMATS: # # (1) VCF-like: chrom pos [ignored] ref alt [ignored] [ignored] [ignored] # examples: # 1 100382042 . C TATC . . . # 1 100382042 . C TATC # 1 100382042 C TATC # # (2) tag-like: chrom|position|ref/alt # examples: # chr1|100382042|C/TATC # # Format (1) can be either space or tab-separated. # All positions are 1-based. # Chromosome names can be prefixed with 'chr'. # Only the GRCh37/hg19 assembly of the human genome is supported. # These lines will be ignored because they start with '#' (hash). # ####################### # SYNONYMOUS VARIANTS # ####################### chr1 173873198 . A G chr2 215819926 . C T chr2 215855594 . C T chr16 16253384 . G A chr16 71602614 . C A chr16 71602170 . A G chr20 10629709 . C A chr20 10637069 . A C chr21 45708253 . C G chr21 5707015 . A T chrX 152034485 . C T chrX 152036178 . G A ##################### # NONSENSE VARIANTS # ##################### chr1 169512110 . G A chr1 169511927 . G A chr1 11253722 . G A chr1 11254607 . C A chr15 40468873 . C T chr15 40476003 . C T chr15 40488843 . C T chr15 40462282 . C T chr15 40750721 . C T chr15 40861573 . G T chrX 3002366 . T A chrX 3021856 . C T chrX 2853025 . G A chrX 2852900 . C T ############## # NFS INDELS # ############## chr1 100346671 . GTTT T chr1 100382042 . C TATC chr1 154570909 . GATG G chr7 27239446 . G GCCGCGGCCGCCGCCGCAG chr7 26192217 . C CCTG chr7 27239320 . G GCAGCGGCAGCCGCGGCAG chr7 91652177 . T TAAA chr7 91652178 . A AAAC chrX 77373600 . AAGG G chrX 79281229 . T AGCT chrX 76944320 . AAGA A chrX 76944375 . T TGTT chrX 77298823 . TCTG G chrX 77298841 . TA AT ############# # FS INDELS # ############# chr1 161044495 . AA A chr1 11082588 . T AT chr12 110019250 . C GC chr12 110969389 . GAAAG G chr12 114836456 . GGTGGCGGGGGAGT T chr13 20797557 . CC C chr15 23021236 . CC C chr15 40764413 . A GTACCGGCCAGCCAGCCCCGA chr15 42691818 . GT T chr17 15406543 . G CTG chr17 17697099 . GCA A chr17 34182100 . T TT chr19 7267604 . TT T chr19 7542175 . T TAT