About vtools_report avg_depth

This command report average depth of all variants, or variants divided by sample allele count.

Usage

% vtools_report avg_depth -h
usage: vtools_report avg_depth [-h] -n NUM_FIELD -d DEPTH_FIELD
                               [--group_by [GROUP_BY [GROUP_BY ...]]]
                               [-v {0,1,2}]
                               table

Command 'vtools update table --from_stat "meanDP=avg(DP_geno)"' calculates the
average depth of variants across sample (e.g. average depth of three variants
if the variant appears three times in the sample). This command report average
depth of all variants, or variants divided by sample allele count (output
count, number of variant, and average depth for count from 1 to 2*#sample).
This command requires a field that stores the sample count for each variant
and a field to store average depth of each variant, which should be prepared
using command 'vtools update table --from_stat "num=#(alt)"
"meanDP=avg(DP_geno)"'.

positional arguments:
  table                 Variant table for which average depth are calculated.

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)"'.
  -d DEPTH_FIELD, --depth_field DEPTH_FIELD
                        Name of the field that holds average depth of each
                        variant, which is the field name for command 'vtools
                        update table --from_stat "meanDP=avg(DP_geno)"'.
  --group_by [GROUP_BY [GROUP_BY ...]]
                        Output average depth for each group, for example, '--
                        group_by NUM_FIELD to output depth for each sample
                        variant frequency (count).
  -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 avg_depth variant -n num -d depth
num_of_variant	average_depth
905	6.86372641088
% vtools_report avg_depth variant -n num -d depth --group_by num
num	num_of_variant	average_depth
1	410	7.18662601626
2	163	32.3737218814
3	28	6.8375
4	72	35.1266203704
5	19	4.93245614035
6	14	4.93571428571
7	23	4.10942028986
... ...