pgxpop_cyp2c19

$ python PGxPOP/bin/PGxPOP.py --vcf chr10_HRC.vcf.gz --gene CYP2C19 --build hg19 --batch --output cyp2c19 --debug


     ________________________________________
    |      ___  ___     ___  ___  ___        |
    |     | _ \/ __|_ _| _ \/\  \| _ \       | 
    |     |  _/ (_ \ \ /  _/  \  |  _/       |
    |     |_|  \___/_\_\_|  \__\/|_|         |
    |                                        |
    |                 v1.0                   |
    |              Written by                |     
    |     Adam Lavertu and Greg McInnes      |
    |        with help from PharmGKB.        |
    |________________________________________|
    
Copyright (C) 2020 Stanford University.
Distributed under the Mozilla Public License 2.0 open source license.
    
Processing CYP2C19
Formatting variants
Alternate build detected.
Alternate genome build found.  Converting positions.
chr10.g.94761900C>T chr10 96521657 rs12248560 C ['T']
Alternate genome build found.  Converting positions.
chr10.g.94762706A>G chr10 96522463 rs28399504 A ['G']
Alternate genome build found.  Converting positions.
chr10.g.94762712C>T chr10 96522469 rs367543002 C ['T']
Alternate genome build found.  Converting positions.
chr10.g.94762715T>C chr10 96522472 rs367543003 T ['C']
Alternate genome build found.  Converting positions.
chr10.g.94762755T>C chr10 96522512 rs55752064 T ['C']
Alternate genome build found.  Converting positions.
chr10.g.94762760A>C chr10 96522517 rs17882687 A ['C']
Alternate genome build found.  Converting positions.
chr10.g.94762788A>T chr10 96522545 None A ['T']
Alternate genome build found.  Converting positions.
chr10.g.94762856A>G chr10 96522613 None A ['G']
Alternate genome build found.  Converting positions.
chr10.g.94775106C>T chr10 96534863 rs145328984 C ['T']
Alternate genome build found.  Converting positions.
chr10.g.94775121C>T chr10 96534878 None C ['T']
Alternate genome build found.  Converting positions.
chr10.g.94775160G>C chr10 96534917 rs118203756 G ['C']
Alternate genome build found.  Converting positions.
chr10.g.94775185A>G chr10 96534942 None A ['G']
Alternate genome build found.  Converting positions.
chr10.g.94775367A>G chr10 96535124 rs12769205 A ['G']
Alternate genome build found.  Converting positions.
chr10.g.94775416T>C chr10 96535173 rs41291556 T ['C']
Alternate genome build found.  Converting positions.
chr10.g.94775453G>A chr10 96535210 rs72552267 G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94775489G>A chr10 96535246 rs17884712 G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94775507G>A chr10 96535264 rs58973490 G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94780574G>C chr10 96540331 rs140278421 G ['C']
Alternate genome build found.  Converting positions.
chr10.g.94780579G>A chr10 96540336 rs370803989 G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94780653G>A chr10 96540410 rs4986893 G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94781858C>T chr10 96541615 rs6413438 C ['T']
Alternate genome build found.  Converting positions.
chr10.g.94781859G>A chr10 96541616 rs4244285 G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94781944G>A chr10 96541701 None G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94781999T>A chr10 96541756 rs72558186 T ['A']
Alternate genome build found.  Converting positions.
chr10.g.94842861G>A chr10 96602618 rs138142612 G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94842879G>A chr10 96602636 rs118203757 G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94842995G>A chr10 96602752 rs113934938 G ['A']
Alternate genome build found.  Converting positions.
chr10.g.94849995C>T chr10 96609752 rs17879685 C ['T']
Alternate genome build found.  Converting positions.
chr10.g.94852738C>T chr10 96612495 rs56337013 C ['T']
Alternate genome build found.  Converting positions.
chr10.g.94852765C>T chr10 96612522 rs192154563 C ['T']
Alternate genome build found.  Converting positions.
chr10.g.94852785C>G chr10 96612542 rs118203759 C ['G']
Alternate genome build found.  Converting positions.
chr10.g.94852914A>C chr10 96612671 rs55640102 A ['C']
Formatting haplotypes
*1 CA100092.1 None
NO MATCH FOUND!
chr10.g.94775507G>A chr10 96535264 rs58973490 G ['A']
[]
['A']
R
Current alt: A
*2 CA100093.1 None
*3 CA100094.1 None
NO MATCH FOUND!
chr10.g.94761900C>T chr10 96521657 rs12248560 C ['T']
[]
['T']
Y
Current alt: T
*4 CA100464.1 None
*5 CA100097.1 None
*6 CA100098.1 None
*7 CA100099.1 None
*8 CA100100.1 None
*9 CA100101.1 None
*10 CA100102.1 None
*11 CA100103.1 None
*12 CA100104.1 None
*13 CA100105.1 None
*14 CA100106.1 None
*15 CA100107.1 None
*16 CA100108.1 None
*17 CA100109.1 None
*18 CA100110.1 None
*19 CA100111.1 None
*22 CA100112.1 None
*23 CA100113.1 None
*24 CA100114.1 None
*25 CA100115.1 None
*26 CA100116.1 None
*28 CA100118.1 None
*29 CA100119.1 None
*30 CA100120.1 None
*31 CA100121.1 None
*32 CA100122.1 None
*33 CA100123.1 None
*34 CA100124.1 None
*35 CA100233.1 None
*2%0 CA100093.1.0 None
*2%1 CA100093.1.1 None
*4%0 CA100464.1.0 None
*4%1 CA100464.1.1 None
Extracting genotype matrices
Genotype extraction finished
Execution time: 0:00:00.005273
Calling diplotypes
Checking for exception file
No exception file found
chr10.g.94761900C>T chr10 96521657 rs12248560 C ['T']
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
T calls found in A: 29
T calls found in B: 19
chr10.g.94762706A>G chr10 96522463 rs28399504 A ['G']
Found alt call
G calls found in A: 0
G calls found in B: 1
chr10.g.94762712C>T chr10 96522469 rs367543002 C ['T']
Variant not found
chr10.g.94762715T>C chr10 96522472 rs367543003 T ['C']
Variant not found
chr10.g.94762755T>C chr10 96522512 rs55752064 T ['C']
Variant not found
chr10.g.94762760A>C chr10 96522517 rs17882687 A ['C']
Variant not found
chr10.g.94762788A>T chr10 96522545 None A ['T']
Variant not found
chr10.g.94762856A>G chr10 96522613 None A ['G']
Variant not found
chr10.g.94775106C>T chr10 96534863 rs145328984 C ['T']
Variant not found
chr10.g.94775121C>T chr10 96534878 None C ['T']
Variant not found
chr10.g.94775160G>C chr10 96534917 rs118203756 G ['C']
Variant not found
chr10.g.94775185A>G chr10 96534942 None A ['G']
Variant not found
chr10.g.94775367A>G chr10 96535124 rs12769205 A ['G']
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
G calls found in A: 25
G calls found in B: 31
chr10.g.94775416T>C chr10 96535173 rs41291556 T ['C']
Found alt call
C calls found in A: 0
C calls found in B: 1
chr10.g.94775453G>A chr10 96535210 rs72552267 G ['A']
Variant not found
chr10.g.94775489G>A chr10 96535246 rs17884712 G ['A']
Variant not found
chr10.g.94775507G>A chr10 96535264 rs58973490 G ['A']
Found alt call
A calls found in A: 1
A calls found in B: 0
chr10.g.94780574G>C chr10 96540331 rs140278421 G ['C']
Variant not found
chr10.g.94780579G>A chr10 96540336 rs370803989 G ['A']
Variant not found
chr10.g.94780653G>A chr10 96540410 rs4986893 G ['A']
Variant not found
chr10.g.94781858C>T chr10 96541615 rs6413438 C ['T']
Variant not found
chr10.g.94781859G>A chr10 96541616 rs4244285 G ['A']
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
Found alt call
A calls found in A: 25
A calls found in B: 31
chr10.g.94781944G>A chr10 96541701 None G ['A']
Variant not found
chr10.g.94781999T>A chr10 96541756 rs72558186 T ['A']
Variant not found
chr10.g.94842861G>A chr10 96602618 rs138142612 G ['A']
Variant not found
chr10.g.94842879G>A chr10 96602636 rs118203757 G ['A']
Variant not found
chr10.g.94842995G>A chr10 96602752 rs113934938 G ['A']
Variant not found
chr10.g.94849995C>T chr10 96609752 rs17879685 C ['T']
Variant not found
chr10.g.94852738C>T chr10 96612495 rs56337013 C ['T']
Variant not found
chr10.g.94852765C>T chr10 96612522 rs192154563 C ['T']
Variant not found
chr10.g.94852785C>G chr10 96612542 rs118203759 C ['G']
Variant not found
chr10.g.94852914A>C chr10 96612671 rs55640102 A ['C']
Variant not found
Traceback (most recent call last):
  File "PGxPOP/bin/PGxPOP.py", line 308, in <module>
    cd.run()
  File "PGxPOP/bin/PGxPOP.py", line 54, in run
    results = self.process_gene(g)
  File "PGxPOP/bin/PGxPOP.py", line 68, in process_gene
    diplotypes, sample_variants, uncallable = self.get_calls(gene, gt_matrices)
  File "PGxPOP/bin/PGxPOP.py", line 177, in get_calls
    for samp in range(gt_mat[0].shape[1]):
IndexError: tuple index out of range