% vtools_report variant_stat -h
usage: vtools_report variant_stat [-h] [-s [SAMPLES [SAMPLES ...]]]
[-g [GROUP_BY [GROUP_BY ...]]] [-v {0,1,2}]
table
Command 'vtools variant_stat' calculates the number of snps, insertions,
deletions and substitutions for groups of samples with some size metrics to
characterize the indels. The statistics can be calculated for all samples
(effectively for the master variant table when parameters --samples and
--group_by are ignored), a subset of samples (e.g. --samples aff=1), grouped
by samples (e.g. --group_by aff), or for each sample separately (e.g.
--group_by filename sample_name, because those two fields in the sample table
uniquely identify each sample.
positional arguments:
table Variant table for which variant metrics are
calculated.
optional arguments:
-h, --help show this help message and exit
-s [SAMPLES [SAMPLES ...]], --samples [SAMPLES [SAMPLES ...]]
Limiting variants from samples that match conditions
that use columns shown in command 'vtools show sample'
(e.g. 'aff=1', 'filename like "MG%"'). If this
parameter is specified without a value, variants
belonging to any of the samples will be counted. If
this parameter is left unspecified, all variants,
including those that do not belong to any samples will
be counted.
-g [GROUP_BY [GROUP_BY ...]], --group_by [GROUP_BY [GROUP_BY ...]]
Group samples by certain conditions such as 'aff=1'. A
common usage is to group variants by 'filename' and
'sample_name' so that variant statistics are outputted
for each sample.
-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.
This command calculates the number of snps, insertions, deletions and substitutions for groups of samples with some size metrics to characterize the indels. You can use parameters --samples to limit variants to specified samples, and --group_by to output statistics for each sample groups. For example, the statistics can be calculated
--samples and --group_by are ignored),--samples aff=1),--group_by aff), or--group_by filename sample_name, because those two fields in the sample table uniquely identify each sample.Note that
% vtools_report variant_stat VTABLE
% vtools_report variant_stat VTABLE --samples 1
% vtools_report variant_stat VTABLE --group_by aff
might give different total variant count because the first command counts all variants in the VTABLE, the second and third commands count all variants in specified samples (all samples for condition 1). Because some variants might not appear in any of the samples, the number of reported variants of the first command might be larger than the others.
You would like to generate output for selected variants (e.g. variants on chromosome 1), you should use command vtools select -t table to generate a variant table and use this command to summarize them.
% vtools_report variant_stat variant --group_by filename
filename num_sample num_snps num_insertions num_deletions num_substitutions min_insertion_size avg_insertion_size max_insertion_size min_deletion_size avg_deletion_size max_deletion_size
case1.vcf 1 21504 322 75 0 1 2.64906832298 23 1 1.28 11
case10.vcf 1 21069 317 77 0 1 2.64353312303 21 1 1.25974025974 6
case11.vcf 1 20995 315 70 0 1 2.65396825397 23 1 1.08571428571 3
case12.vcf 1 22195 340 68 0 1 2.91176470588 26 1 1.23529411765 10
... ...