gpcr
commented
8 years ago It worked after adjusting assembly and other minor fixes in the b37 definition files i created:
PharmCAT Allele Call Report for test.vcf CFTR Definition Position 117188682 VCF Position 117188682 VCF REF,ALTs G,GTT VCF Call G/GTT Reference G(T)7A 5T G(T)5A There were 33 missing positions from the VCF file:
117246808 (g.117246808G>A) 117227860 (g.117227860G>A) 117174372 (g.117174372G>A) 117227865 (g.117227865C>T) 117267591 (g.117267591C>T) 117282620 (g.117282620G>A) 117230494 (g.117230494G>A) 117282537 (g.117282537T>C) 117171029 (g.117171029G>A) 117174420 (g.117174420G>T) 117180284 (g.117180284C>T) 117199645 (g.117199646_117199648delCTT) 117227832 (g.117227832G>T) 117304824 (g.117304824G>A) 117267634 (g.117267635delC) 117171169 (g.117171169G>T) 117242922 (g.117242922G>A) 117227853 (g.117227853A>C) 117227887 (g.117227887G>C) 117227859 (g.117227859G>A) 117232272 (g.117232273delA) 117227855 (g.117227855T>G) 117199644 (g.117199645_117199647delTCT) 117280015 (g.117280015C>T) 117180324 (g.117180324G>C) 117227854 (g.117227854G>A) 117292931 (g.117292931C>G) 117282526 (g.117282526G>A) 117188849 (g.117188849C>A) 117227792 (g.117227792G>A) 117282505 (g.117282505G>A) 117149177 (g.117149177G>A) 117199643 (g.117199644_117199646delATC) The following haplotype(s) were eliminated from consideration:
2789+5G->A 1717-1G->A S549R(T>G) R560T 711+1G->T S549N G542X R334W 1898+1G->A S1255P S1251N 621+1G->T W1282X G551D N1303K R1162X A455E 3120+1G->A G85E F508del(TCT) G1349D G551S F508del(CTT) 3849+10kbC- >T R553X G1244E 3659delC I507 2184delA R347P G178R R117H S549R(A>C) CYP2C19 _1/_2 (4) _2/_35 (3) Definition Position 96535124 96541616 rs12769205 rs4244285 VCF Position 96535124 96541616 VCF REF,ALTs A,G G,A VCF Call A/G G/A 1 A G A G 2 [AG] A A A G A *35 G G G G There were 36 missing positions from the VCF file:
96535210 (g.96535210G>A) 96521422 (g.96521422G>A) 96522613 (g.96522613A>G) 96541701 (g.96541701G>A) 96520433 (g.96520433C>T) 96522469 (g.96522469C>T) 96522512 (g.96522512T>C) 96540331 (g.96540331G>C) 96612495 (g.96612495C>T) 96612671 (g.96612671A>C) 96535173 (g.96535173T>C) 96602636 (g.96602636G>A) 96520443 (g.96520443C>A) 96540336 (g.96540336G>A) 96522463 (g.96522463A>G) 96609721 (g.96609721A>G) 96535264 (g.96535264G>A) 96534942 (g.96534942A>G) 96540410 (g.96540410G>A) 96521024 (g.96521024T>C) 96534863 (g.96534863C>T) 96602618 (g.96602618G>A) 96541756 (g.96541756T>A) 96522472 (g.96522472T>C) 96522517 (g.96522517A>C) 96522450 (g.96522450G>A) 96609752 (g.96609752C>T) 96612522 (g.96612522C>T) 96541615 (g.96541615C>T) 96535246 (g.96535246G>A) 96602752 (g.96602752G>A) 96521657 (g.96521657C>T) 96534878 (g.96534878C>T) 96522545 (g.96522545A>T) 96534917 (g.96534917G>C) 96612542 (g.96612542C>G) The following haplotype(s) were eliminated from consideration:
30 31 3 10 32 11 33 5 12 34 6 13 7 14 8 15 9 16 17 18 19 22 23 24 25 26 27 28 29 4A *4B The following haplotypes were called even though tag positions were missing:
Called *1 without g.96520433C>T, g.96520443C>A, g.96521024T>C, g.96521422G>A, g.96521657C>T, g.96522450G>A, g.96522463A>G, g.96522469C>T, g.96522472T>C, g.96522512T>C, g.96522517A>C, g.96522545A>T, g.96522613A>G, g.96534863C>T, g.96534878C>T, g.96534917G>C, g.96534942A>G, g.96535173T>C, g.96535210G>A, g.96535246G>A, g.96535264G>A, g.96540331G>C, g.96540336G>A, g.96540410G>A, g.96541615C>T, g.96541701G>A, g.96541756T>A, g.96602618G>A, g.96602636G>A, g.96602752G>A, g.96609721A>G, g.96609752C>T, g.96612495C>T, g.96612522C>T, g.96612542C>G, g.96612671A>C CYP2C9 Definition Position VCF Position VCF REF,ALTs VCF Call There were 54 missing positions from the VCF file:
96707664 (g.96707664A>C) 96698528 (g.96698528C>T) 96731891 (g.96731891A>G) 96731937 (g.96731937C>G) 96702047 (g.96702047C>T) 96701733 (g.96701733G>C) 96701672 (g.96701672G>A) 96707542 (g.96707542C>T) 96741059 (g.96741059C>A) 96741038 (g.96741038G>A) 96701715 (g.96701715T>C) 96702066 (g.96702066G>A;g.94942309G>T) 96698494 (g.96698494C>A) 96741058 (g.96741058C>G) 96745799 (g.96745799A>G) 96701969 (g.96701970_96701979delAGAAATGGAA) 96707695 (g.96707695A>T) 96748737 (g.96748737A>T) 96708901 (g.96708901C>T) 96748674 (g.96748674G>C) 96701991 (g.96701991G>A) 96702062 (g.96702062G>A) 96748777 (g.96748777C>T) 96707539 (g.96707539C>A) 96701654 (g.96701654G>C) 96702006 (g.96702006C>T;g.94942249C>G) 96707674 (g.96707674T>C) 96701775 (g.96701775T>C) 96702011 (g.96702011C>T) 96741007 (g.96741007C>A) 96741053 (g.96741053A>C) 96701739 (g.96701739G>T) 96731936 (g.96731936A>G) 96709038 (g.96709039delA) 96709037 (g.96709037A>G) 96731876 (g.96731876C>A) 96740982 (g.96740982G>A) 96708886 (g.96708886A>G) 96740981 (g.96740981C>T) 96698440 (g.96698440A>G) 96701988 (g.96701988G>A) 96741122 (g.96741122C>T) 96701973 (g.96701973A>G) 96731990 (g.96731990C>T) 96745830 (g.96745830A>C) 96748780 (g.96748780G>T) 96698585 (g.96698585A>G) 96708974 (g.96708974A>G) 96740958 (g.96740958T>C) 96698560 (g.96698560A>G) 96702012 (g.96702012G>A) 96701987 (g.96701987C>T) 96741054 (g.96741054T>C) 96748741 (g.96748741G>A) The following haplotype(s) were eliminated from consideration:
30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 1 52 2 53 3 10 54 4 11 55 5 12 56 6 13 57 7 14 8 15 9 16 17 18 19 20 21 22 23 24 25 26 27 28 *29 CYP3A5 Definition Position VCF Position VCF REF,ALTs VCF Call There were 8 missing positions from the VCF file:
99262860 (g.99262860T>C) 99258139 (g.99258139C>T) 99270539 (g.99270539T>C) 99264573 (g.99264573A>G) 99262835 (g.99262835C>T) 99250236 (g.99250236G>T) 99250393 (g.99250393_99250394insA) 99273821 (g.99273821G>A) The following haplotype(s) were eliminated from consideration:
_1 2 3 4 5 6 7 8 9 DPYD 1/_4 (3) Definition Position 97981421 98348885 rs1801158 rs1801265 VCF Position 97981421 98348885 VCF REF,ALTs C,T G,A VCF Call C/T A|A 1 C A C A *4 T A T A There were 13 missing positions from the VCF file:
97915614 (g.97915614C>T) 98205970 (g.98205971_98205974delATGA) 98039499 (g.98039499C>A) 97547947 (g.97547947T>A) 97915621 (g.97915622delG) 97981395 (g.97981395T>C) 97544627 (g.97544627C>A) 98348908 (g.98348908C>T) 97770920 (g.97770920C>T) 97564154 (g.97564154C>T) 98058899 (g.98058899C>A) 98157332 (g.98157332G>A) 97981343 (g.97981343A>C) The following haplotype(s) were eliminated from consideration:
rs67376798T/A 2A 3 10 2B 11 5 12 6 13 7 *8 The following haplotypes were called even though tag positions were missing:
Called *1 without g.97544627C>A, g.97547947T>A, g.97564154C>T, g.97770920C>T, g.97915614C>T, g.97915622delG, g.97981343A>C, g.97981395T>C, g.98039499C>A, g.98058899C>A, g.98157332G>A, g.98205971_98205974delATGA, g.98348908C>T IFNL3 Definition Position VCF Position VCF REF,ALTs VCF Call There was 1 missing positions from the VCF file:
39738787 (g.39738787C>T) The following haplotype(s) were eliminated from consideration:
rs12979860C rs12979860T SLCO1B1 Definition Position 21329738 21329761 21329813 21331599 21331625 rs2306283 rs11045818 rs11045819 rs4149057 rs2291075 VCF Position 21329738 21329761 21329813 21331599 21331625 VCF REF,ALTs A,G G,A C,A T,C C,T VCF Call G|G A|A A|A C|C T|T 1A A G C T C 1B G G C T C 4 A G A T C 14 G G A T C 15 G G C T C 17 G G C T C 18 G A A C C 19 A G C C C 20 G G C T T 21 G G C T T 24 G G C T C 25 G G A T C 27 G G C T C 28 G G C T C 29 G G C T C 30 G G C T C 31 G G C T C 32 G G A T C 33 G G C T C 35 G G C T C There were 24 missing positions from the VCF file:
21283322 (g.21283322G>A) 21392011 (g.21392011A>G) 21327529 (g.21327529T>C) 21349885 (g.21349885A>G) 21349910 (g.21349910G>A) 21391976 (g.21391976A>C) 21353529 (g.21353529T>C) 21325710 (g.21325710G>A) 21325716 (g.21325716T>C) 21355598 (g.21355598G>A) 21325668 (g.21325668C>T) 21331549 (g.21331549T>C) 21358855 (g.21358855A>G) 21392092 (g.21392092C>T) 21355489 (g.21355489C>G) 21355487 (g.21355487T>G) 21358933 (g.21358933G>C) 21329802 (g.21329802A>G) 21329817 (g.21329817A>G) 21331606 (g.21331606T>G) 21331891 (g.21331891A>G) 21392047 (g.21392047A>G) 21355583 (g.21355583A>G) 21392079 (g.21392079C>T) The following haplotype(s) were eliminated from consideration:
2 3 10 11 22 5 12 23 34 6 13 7 36 8 26 9 16 TPMT Definition Position 18130918 18139214 18139228 rs1142345 rs2842934 rs1800460 VCF Position 18130918 18139214 18139228 VCF REF,ALTs T,C G,A C,T VCF Call T/C A|A C/T 1 T G C 1S T A C 3A C G T 3B T G T 3C C G C There were 28 missing positions from the VCF file:
18131003 (g.18131003A>G) 18134121 (g.18134121C>T) 18139258 (g.18139258C>G) 18149235 (g.18149235G>C) 18131012 (g.18131012C>T) 18148141 (g.18148141A>G) 18143844 (g.18143844C>G) 18149357 (g.18149357A>G) 18134078 (g.18134078C>A) 18134076 (g.18134076T>A) 18134115 (g.18134115G>C) 18132378 (g.18132378A>G) 18130956 (g.18130956A>C) 18149276 (g.18149276T>A) 18143955 (g.18143955C>G) 18148076 (g.18148076C>T) 18132367 (g.18132367A>G) 18130993 (g.18130993C>T) 18139920 (g.18139920C>T) 18130925 (g.18130925T>C) 18143828 (g.18143828T>G) 18143874 (g.18143874A>C) 18139200 (g.18139200C>T; g.18138969C>G) 18148082 (g.18148082G>C) 18143837 (g.18143837T>G) 18139941 (g.18139941G>A) 18149358 (g.18149358T>C) 18149253 (g.18149253C>T) The following haplotype(s) were eliminated from consideration:
30 2 31 10 4 11 5 12 6 13 7 14 8 15 9 16 17 18 19 20 21 22 23 24 25 26 27 28 *29 UGT1A1 Definition Position VCF Position VCF REF,ALTs VCF Call There were 5 missing positions from the VCF file:
234668570 (g.234668570C>T) 234665659 (g.234665659T>G) 234668880 (g.234668880) 234669144 (g.234669144G>A) 234669619 (g.234669619C>A) The following haplotype(s) were eliminated from consideration:
28 80 60 1 6 36 37 27 VKORC1 -1639A/-1639G (2) Definition Position 31107689 rs9923231 VCF Position 31107689 VCF REF,ALTs C,T VCF Call C/T -1639A T T -1639G C C Generated on 08/07/16.
markwoon
I am trying to run through NamedAlleleMatcher using grch37 files i generated
All the out puts says missing.....
Can you add explample files to run and test. Thanks ........................
There were 38 missing positions from the VCF file: CYP2C19 Definition Position VCF Position VCF REF,ALTs VCF Call 96535210 (g.96535210G>A) 96521422 (g.96521422G>A) 96522613 (g.96522613A>G) 96541701 (g.96541701G>A) 96520433 (g.96520433C>T) 96522469 (g.96522469C>T) 96522512 (g.96522512T>C) 96540331 (g.96540331G>C) 96541616 (g.96541616G>A) 96612495 (g.96612495C>T) 96612671 (g.96612671A>C) 96535173 (g.96535173T>C) 96602636 (g.96602636G>A) 96535124 (g.96535124A>G) 96520443 (g.96520443C>A) 96540336 (g.96540336G>A) 96522463 (g.96522463A>G) 96609721 (g.96609721A>G) 96535264 (g.96535264G>A) 96534942 (g.96534942A>G) 96540410 (g.96540410G>A) 96521024 (g.96521024T>C) 96534863 (g.96534863C>T) 96602618 (g.96602618G>A) 96541756 (g.96541756T>A) 96522472 (g.96522472T>C) 96522517 (g.96522517A>C) 96522450 (g.96522450G>A) 96609752 (g.96609752C>T) 96612522 (g.96612522C>T) 96541615 (g.96541615C>T) 96535246 (g.96535246G>A) 96602752 (g.96602752G>A) 96521657 (g.96521657C>T) 96534878 (g.96534878C>T) 96522545 (g.96522545A>T) 96534917 (g.96534917G>C) 96612542 (g.96612542C>G) The following haplotype(s) were eliminated from consideration:
1 30 2 31 3 10 32 11 33 5 12 34 6 13 35 7 14 8 15 9 16 17 18 19 22 23 24 25 26 27 28 29 4A 4B