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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.
usage: consistency [-h] [-d] [-j] [-o OUTPUT] 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
-d, --no-dups Disallow duplicate SVs
-j, --json Output report in json format
-o OUTPUT, --output OUTPUT
Write tsv of variant keys and their flag
truvari consistency fileA.vcf fileB.vcf fileC.vcfVCF 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. The key and flags can be written with the --output option.
If there are VCFs with duplicate keys, they are handled by appending a e.g. .1 to the key. If you'd like to ignore duplicates, just add --no-dups
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.
Below is a consistency report in json format.
{
"vcfs": [
"repo_utils/test_files/variants/input1.vcf.gz",
"repo_utils/test_files/variants/input2.vcf.gz",
"repo_utils/test_files/variants/input3.vcf.gz"
],
"total_calls": 3513,
"num_vcfs": 3,
"vcf_counts": {
"repo_utils/test_files/variants/input1.vcf.gz": 2151,
"repo_utils/test_files/variants/input2.vcf.gz": 1783,
"repo_utils/test_files/variants/input3.vcf.gz": 2065
},
"shared": [
{
"vcf_count": 3,
"num_calls": 701,
"call_pct": 0.1995445488186735
},
{
"vcf_count": 2,
"num_calls": 1084,
"call_pct": 0.3085681753487048
},
{
"vcf_count": 1,
"num_calls": 1728,
"call_pct": 0.4918872758326217
}
],
"detailed": [
{
"group": "111",
"total": 701,
"total_pct": 0.1995445488186735,
"repo_utils/test_files/variants/input1.vcf.gz": 0.32589493258949326,
"repo_utils/test_files/variants/input2.vcf.gz": 0.393157599551318,
"repo_utils/test_files/variants/input3.vcf.gz": 0.3394673123486683
},
{
"group": "001",
"total": 645,
"total_pct": 0.18360375747224594,
"repo_utils/test_files/variants/input1.vcf.gz": 0,
"repo_utils/test_files/variants/input2.vcf.gz": 0,
"repo_utils/test_files/variants/input3.vcf.gz": 0.31234866828087166
},
{
"group": "100",
"total": 598,
"total_pct": 0.17022487902077996,
"repo_utils/test_files/variants/input1.vcf.gz": 0.2780102278010228,
"repo_utils/test_files/variants/input2.vcf.gz": 0,
"repo_utils/test_files/variants/input3.vcf.gz": 0
},
{
"group": "101",
"total": 487,
"total_pct": 0.1386279533162539,
"repo_utils/test_files/variants/input1.vcf.gz": 0.22640632264063226,
"repo_utils/test_files/variants/input2.vcf.gz": 0,
"repo_utils/test_files/variants/input3.vcf.gz": 0.2358353510895884
},
{
"group": "010",
"total": 485,
"total_pct": 0.13805863933959578,
"repo_utils/test_files/variants/input1.vcf.gz": 0,
"repo_utils/test_files/variants/input2.vcf.gz": 0.27201346045989905,
"repo_utils/test_files/variants/input3.vcf.gz": 0
},
{
"group": "110",
"total": 365,
"total_pct": 0.10389980074010817,
"repo_utils/test_files/variants/input1.vcf.gz": 0.1696885169688517,
"repo_utils/test_files/variants/input2.vcf.gz": 0.2047111609646663,
"repo_utils/test_files/variants/input3.vcf.gz": 0
},
{
"group": "011",
"total": 232,
"total_pct": 0.06604042129234272,
"repo_utils/test_files/variants/input1.vcf.gz": 0,
"repo_utils/test_files/variants/input2.vcf.gz": 0.13011777902411667,
"repo_utils/test_files/variants/input3.vcf.gz": 0.11234866828087167
}
]
}