SnpSift Concordance
Calculate concordance between two VCF files.
Typical usage
This is typically used when you want to calculate concordance between a genotyping experiment and a sequencing experiment.
For instance, you sequenced several samples and, as part of a related experiment or just as quality control, you also genotype the same samples using a genotyping array. Now you want to compare the two experiments. Ideally there would be no difference between the variants from genotyping and sequencing, but this is hardly the case in real world.
You can use SnpSift concordance to measure the differences between the two experiments.
Warning
It is assumed that both VCF files are sorted by chromosome and position.
Warning
Sample names are defined in '#CHROM' line of the header section. Concordance is calculated only if sample label matches in both files.
Example:
$ java -Xmx1g -jar SnpSift.jar concordance -v genotype.vcf sequencing.vcf > concordance.txt
00:00:00.000 Indexing file 'genotype.vcf'
index: MT 460030998
index: 1 19705
1 / 2 45170805 / 45174315
2 / 3 77052081 / 77055591
3 / 4 104065531 / 104069041
4 / 5 124098372 / 124101881
5 / 6 146535292 / 146538802
6 / 7 184793526 / 184797035
7 / 8 206156508 / 206160018
8 / 9 223072816 / 223076326
9 / 10 242315995 / 242319505
10 / 11 261053789 / 261057299
11 / 12 290190553 / 290194063
12 / 13 312869636 / 312873146
13 / 14 321966539 / 321970049
14 / 15 336131317 / 336134827
15 / 16 350871669 / 350875179
16 / 17 368900523 / 368904032
17 / 18 391305860 / 391309369
18 / 19 398932237 / 398935747
19 / 20 425219198 / 425222708
20 / 21 437022008 / 437025517
21 / 22 442563678 / 442567188
22 / X 451783418 / 451786927
X / Y 459553691 / 459557200
Y / MT 459588787 / 459592296
00:00:01.137 Open VCF file 'genotype.vcf'
00:00:01.141 Open VCF file 'sequencing.vcf'
00:00:01.176 Chromosome: '1'
00:00:02.127 1:1550992 1:1528859
00:00:02.739 1:2426313 1:2389636
...
00:02:13.780 1:248487058 1:248471945
Output
SnpSift's concordance output is written to STDOUT and two files.
For instance the command java -jar SnpSift.jar concordance -v genotype.vcf sequencing.vcf will write:
- Concordance by variant: Written to STDOUT
- Concordance by sample: Written to
concordance_genotyping_sequencing.by_sample.txt - Summary: Written to
concordance_genotyping_sequencing.summary.txt
Concordance by variant
This sections is a table showing concordance details for every entry (chr:position) that both files have in common. E.g.:
chr pos ref alt change_0_0 change_0_1 change_0_2 change_1_0 change_1_1 change_1_2 change_2_0 change_2_1 change_2_2 missing_genotype_genotype missing_genotype_sequencing
1 865584 G A 508 0 0 0 2 0 0 0 0 0 5
1 865625 G A 512 0 0 0 1 0 0 0 0 0 1
1 865628 G A 511 0 0 0 2 0 0 0 0 0 1
1 865665 G A 495 0 0 0 4 0 0 0 0 0 17
1 865694 C T 428 0 0 0 82 0 0 0 4 0 0
- '0/0' (homozygous reference) is coded as '0'
- '0/1' or '1/0' (heterozygous ALT) coded as '1'
- '1/1' (homozygous ALT) is coded as '1'
So the column "change_X_Y" on the table shows how many genotypes coded 'X' in the first VCF, changed to 'Y' in the second VCF. For example, 'change_0_1' counts the number of "homozygous reference in genotype.vcf" that changed to "heterozygous ALT in sequencing.vcf". Or 'change_2_2' counts the number of "homozygous ALT" that did not change (in both files they are '2').
A few rules apply:
- If a VCF entry (chr:pos) is present in only one of the files, obviously we cannot calculate concordance, so it is ignored.
- If a VCF entry (chr:pos) has more than one ALT it is ignored. This means that non-biallelic variants are ignored.
- If, for the same chr:pos, REF field is different between the two files, then the entry is ignored.
- If, for the same chr:pos, ALT field is different between the two files, then the entry is ignored.
Concordance by sample
This section shows details in the same format as the previous section. Here, concordance metrics are shown aggregated for each sample. E.g.:
# Totals by sample
sample change_0_0 change_0_1 change_0_2 change_1_0 change_1_1 change_1_2 change_2_0 change_2_1 change_2_2 missing_genotype_genotype missing_genotype_sequencing
ID_003 79 0 0 1 8 0 0 0 2 1 1
ID_004 83 0 0 1 2 0 0 0 5 0 1
ID_005 80 0 0 0 7 0 0 0 4 1 0
ID_006 79 0 0 0 5 0 0 0 6 0 2
ID_008 81 0 0 0 4 0 0 0 4 0 3
ID_009 80 0 0 0 7 0 0 0 3 0 2
ID_012 74 0 0 0 10 0 0 0 1 0 7
ID_013 79 1 0 0 4 0 0 0 5 0 3
ID_018 84 0 0 0 5 0 0 0 3 0 0
...
Summary
Summary file contains overall information and errors. Here is an example of a summary file:
$ cat concordance_genotyping_sequencing.summary.txt
Number of samples:
929 File genotype.vcf
583 File sequencing.vcf
514 Both files
Errors:
ALT field does not match 19
At the end of the file, a footer shows the total for each column followed by number of possible errors (or mismatches). In this case the were 19 ALT fields that did not match between 'genotype.vcf' and 'sequencing.vcf'. This can happen, for instance, when there are INDELs, which cannot be detected by genotyping arrays.
Info
Summary messages are shown to STDERR if you use verbose mode (command line option -v).