Converts a sample of sites from standard VCF table into tidy format for easy summary stats and plotting.
It's often desirable to get a sense of the site and genotype metrics from a VCF file prior to filtering. This simple program is designed to faciltate that. While there are excellent tools like bcftools stats to do this already, the summary statistics gathered are very simple and not very customizable. If you don't mind exchanging speed for more information and flexibility, give this tool a try.
The program determines the data frame features based on the FORMAT and INFO listed in the VCF header. The output features depend on what is listed in the header. When an individual site does not contain a particular INFO feature, an NA is added to the row of that feature. This means the output data frames should contain all the information in the original. It also means the VCF header that faithfully represents what is present in the VCF rows is absolutely essential.
Depends on python3 with the argparse, gzip, and random libraries available.
pip install tidy-vcf
usage: tidy-vcf [-h] [-s [SITES]] [-t THIN] -v [VCF] -o [SITES_OUT] -g
[GENOTYPE_OUT]
Given a vcf file, produces a tidy versions of sites and genotypes data, in
efforts to make it easier to calculate summary statitics and visualizations.
optional arguments:
-h, --help show this help message and exit
-s [SITES], --sites [SITES]
Input file listing tab delimited sites to output. Each
line must be a chromosome/scaffold name and the
1-indexed position of the site.
-t THIN, --thin THIN Alternative to --sites, where a sites will be selected
no less than THIN bases apart.
-v [VCF], --vcf [VCF]
VCF input file. Should end in .vcf or .gz (plain text
or compressed).
-o [SITES_OUT], --sites_out [SITES_OUT]
Name of output file for tidy sites data. Cannot be
used simultaneously with --thin
-g [GENOTYPE_OUT], --genotype_out [GENOTYPE_OUT]
Name of output file for tidy genotype data.
This repo contains necessary examples to test out the utility, but three example commands assume you have installed the program using pip above.
For example sites.txt contains 1,000 sites, the following command will generate to two tidy data files:
tidy-vcf -s example/sites.txt -v example/test.vcf.gz -o example/test_tidy_sites.vcf -g example/test_tidy_genotypes.vcf
Alternatively, you can also using the -t argument, which specifies how far apart sampled positions should be:
tidy-vcf -t 1000 -v example/test.vcf.gz -o example/test_tidy_sites.vcf -g example/test_tidy_genotypes.vcf
Alternatively, you can use neither -t or -s, in which case all sites will be used with a warning:
tidy-vcf -v example/test.vcf.gz -o example/test_tidy_sites.vcf -g example/test_tidy_genotypes.vcf
The sites and genotypes file are easy to load into R or Python for summary and visualzation.
Here's a simple example that can be done in R:
#Read sites data
sites <- vroom::vroom("example/test_tidy_sites.vcf", delim = "\t", na = c("NA", "./.", '.'), comment = "#")
head(sites)
# A tibble: 6 x 23
CHROM POS ID REF ALT QUAL FILTER AC AF AN BaseQRankSum ClippingRankSum DP ExcessHet
<chr> <dbl> <lgl> <chr> <chr> <dbl> <lgl> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 chr1 4240 NA TC T,CC 302. NA 113 0.01… 62 0.277 0 179 3.13
2 chr1 4248 NA A G 3303. NA 68 1.000 68 NA NA 186 3.01
3 chr1 4261 NA C T 113. NA 15 0.214 70 -3.37 0 218 0
4 chr1 4375 NA C T 41.3 NA 2 0.007 284 0.089 0 878 0.0077
5 chr1 4441 NA G A 110. NA 2 0.021 96 0.713 0 212 0.0229
6 chr1 4495 NA C T 280. NA 21 0.250 84 2.07 0 130 0.0017
# … with 9 more variables: FS <dbl>, InbreedingCoeff <dbl>, MLEAC <dbl>, MLEAF <chr>, MQ <dbl>, MQRankSum <dbl>,
# QD <dbl>, ReadPosRankSum <dbl>, SOR <dbl>
#Read genotype data
genos <-vroom::vroom("example/test_tidy_genotypes.vcf", delim = "\t", na = c("NA", "./.", '.'), comment = "#")
head(genos)
# A tibble: 6 x 13
IND CHROM POS ID REF ALT QUAL FILTER GT AD DP GQ PL
<chr> <chr> <dbl> <lgl> <chr> <chr> <dbl> <lgl> <chr> <chr> <dbl> <dbl> <chr>
1 JRIAL10-10 chr1 4240 NA TC T,CC 302. NA NA NA 0 0 NA
2 JRIAL10-11 chr1 4240 NA TC T,CC 302. NA NA NA 0 0 NA
3 JRIAL10-12 chr1 4240 NA TC T,CC 302. NA NA NA 0 0 NA
4 JRIAL10-13 chr1 4240 NA TC T,CC 302. NA NA NA 0 0 NA
5 JRIAL10-14 chr1 4240 NA TC T,CC 302. NA NA NA 0 0 NA
6 JRIAL10-15 chr1 4240 NA TC T,CC 302. NA NA NA 0 0 NA
#For each individual, summarize average proportion of missing genotypes, and average and standard deviation of depth and genotype quality.
genos %>%
group_by(IND) %>%
summarise(
missing = mean(is.na(GT)),
dp = mean(DP),
dp_std = sd(DP),
gq = mean(GQ),
gq_std = sd(GQ)
)
# A tibble: 195 x 6
IND missing dp dp_std gq gq_std
<chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 JRIAL1-1 0.706 1.05 2.44 3.71 9.80
2 JRIAL1-10 0.753 0.662 1.69 2.37 7.03
3 JRIAL1-11 0.633 1.77 3.93 5.67 13.0
4 JRIAL1-12 0.701 1.18 2.85 3.99 10.5
5 JRIAL1-13 0.662 1.31 2.92 4.49 11.1
6 JRIAL1-14 0.693 1.07 2.43 3.78 9.99
7 JRIAL1-15 0.595 1.15 2.09 3.91 7.93
8 JRIAL1-16 0.722 0.788 1.88 2.70 7.74
9 JRIAL1-17 0.675 1.13 2.44 3.96 9.81
10 JRIAL1-18 0.714 0.848 2.05 2.96 8.00
# … with 185 more rows
Unless a set of sites is of interest, it probably makes more sense to use the --thin flag. However, if you don't want to use --thin one way to get a random set would be:
zcat < example/test.vcf.gz | grep -v "#" | cut -f1,2 | shuf -n 100 | sort -V > sites.txt
where shuf -n could be modified to a desired number. If your VCF is very large, another approach to get a set would likely be needed.