Description Usage Arguments Value Note Examples
Extract read counts from VCF file of a single sample.
1 | extractCoverageFromVcf(vcfFileName, ADFieldIndex = 2)
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vcfFileName |
Path of the VCF file. |
ADFieldIndex |
Index of the AD field of the sample field. For example, if the format is "GT:AD:DP:GQ:PL", the AD index is 2 (by default). |
A data.frame contains four columns: chromosomes, positions, reference allele count, alternative allele count.
The VCF file should only contain one sample. If more samples present in the VCF, it only returns coverage for of the first sample.
1 2 | vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390 = extractCoverageFromVcf(vcfFile)
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