consistency

In addition to looking at performance of a single set of variation against a baseline, one may wish to measure the consistency between multiple sets of variation. The tool truvari consistency can automatically create that result.

Running

usage: consistency [-h] VCFs [VCFs ...]

Over multiple vcfs, calculate their intersection/consistency.

Calls will match between VCFs if they have a matching key of:
    CHROM:POS ID REF ALT

positional arguments:
  VCFs        VCFs to intersect

optional arguments:
  -h, --help  show this help message and exit

Example

truvari consistency fileA.vcf fileB.vcf fileC.vcf

Matching Entries

VCF entries will be considered matching if and only if they have an exact same key of CHROM:POS ID REF ALT. Because of this stringency, it is recommend that you compare the tp-base.vcf or fn.vcf results from each individual VCF's Truvari output.

Output Report

Below is an example report:

#
# Total 5534 calls across 3 VCFs
#
#File	NumCalls
fileA.vcf	4706
fileB.vcf	4827
fileC.vcf	4882
#
# Summary of consistency
#
#VCFs	Calls	Pct
3	3973	71.79%
2	935	16.90%
1	626	11.31%
#
# Breakdown of VCFs' consistency
#
#Group	Total	TotalPct	PctOfFileCalls
111	3973	71.79%	84.42% 82.31% 81.38%
011	351	6.34%	7.27% 7.19%
101	308	5.57%	6.54% 6.31%
110	276	4.99%	5.86% 5.72%
001	250	4.52%	5.12%
010	227	4.10%	4.70%
100	149	2.69%	3.17%

At the top we see that we compared 5,534 unique variants between the 3 files, with fileC.vcf having the most calls at 4,882.

The "Summary of consistency" shows us that 3,973 (71.79%) of all the calls are shared between the 3 VCFs, while 626 (11.31%) are only found in one of the VCFs.

Reading the "Breakdown of VCFs' consistency", a Group is a unique key for presence (1) or absence (0) of a call within each of the listed #Files. For example: Group 111 is calls present in all VCFs; Group 011 is calls present in only the 2nd and 3rd VCFs (i.e. fileB.vcf and fileC.vcf).

We see that Group 101 has calls belonging to the 1st and 3rd #Files (i.e. fileA.vcf and fileC.vcf). This group has a total of 308 calls that intersect, or 5.57% of all calls in all VCFs. This 308 represents 6.54% of calls in fileA.vcf and 6.31% of calls in fileC.vcf.

Finally, we see that fileA.vcf has the least amount of calls unique to it on the Group 100 line.