Calculate various per sample statistics from a VCF file

Only biallelic SNPs are considered. For each sample, the following statistics are calculated :

• INDIV : Sample name

• N_SITES : Total number of SNPs

• N_HET : Number of SNPs with heterozygous call (0/1 or 0|1 or 1/0 or 1|0)

• N_ALT : Number of SNPs with alternate homozygous call (1/1 or 1|1)

• N_REF : Number of SNPs with reference homozygous call (0/0 or 0|0)

• N_MISS : Number of SNPs with missing call (./. or .|.)

• P_HET : Percentage of heterozygous calls

• P_ALT : Percentage of alternate homozygous calls

• P_REF : Percentage of reference homozygous calls

• P_MISS : Percentage of missing calls (missing rate)

Usage

vcf2istats(inputFile, outputFile = NULL)

Arguments

inputFile

Input vcf file location (uncompressed or gzip compressed).

outputFile

Output samples statistics file location.

Value

A data.frame of sample statistics.

References

Java implementation: https://github.com/gkanogiannis/BioInfoJava-Utils

Author

Anestis Gkanogiannis, anestis@gkanogiannis.com

Examples

my.istats <- vcf2istats(
    inputFile =
        system.file("extdata", "samples.vcf.gz", package = "fastreeR")
)