vtools_report trans_ratio This command counts the number of transition and transversion variants and calculates its ratio. The expected ratio is 2 in human pseudo-genes (after the exclusion of transitions at CpG sites).
% vtools_report trans_ratio -h
usage: vtools_report trans_ratio [-h] -n NUM_FIELD
[--group_by [GROUP_BY [GROUP_BY ...]]]
[-v {0,1,2}]
table
This command counts the number of transition (A<->G and C<->T) and
transversion variants (others) and calculate its ratio. A ratio of 2 is
expected from a normal sample. If option '--by_count' is specified, it will
calculate this ratio for variants with different sample allele frequency
(count). This commands requires a field that stores the sample count for each
variant, which should be prepared using command 'vtools update table
--from_stat "num=#(alt)"'.
positional arguments:
table Variant table for which transversion/transversion
mutants are counted.
optional arguments:
-h, --help show this help message and exit
-n NUM_FIELD, --num_field NUM_FIELD
Name of the field that holds sample variant count,
which is the field name for command 'vtools update
table --from_stat "num=#(alt)"'.
--group_by [GROUP_BY [GROUP_BY ...]]
Output transition/transversion rate for groups of
variants. e.g. --group_by num for each sample variant
frequency group.
-v {0,1,2}, --verbosity {0,1,2}
Output error and warning (0), info (1) and debug (2)
information of vtools and vtools_report. Debug
information are always recorded in project and
vtools_report log files.
% vtools_report trans_ratio variant -n num
num_of_transition num_of_transversion ratio
4891 2562 1.909
% vtools_report trans_ratio variant -n num --group_by num
sample_count num_of_transition num_of_transversion ratio
1 375 170 2.206
2 105 68 1.544
3 17 8 2.125
4 44 25 1.760
5 15 3 5.000
6 10 11 0.909
7 9 6 1.500
8 12 7 1.714
9 8 7 1.143
10 4 6 0.667
... ...