About 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).

Usage

% 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.

Example

% 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
... ...