readGenoDoseFileFromBcftools | R Documentation |
Read an input file with genotypes as allele dosage as written by bcftools +dosage genos.vcf.gz | tr ' ' '\t' | datamash transpose | gzip > genos_dosage.tsv.gz
.
Caution, depending on the file size, this may require the allocation of too much RAM for your system.
readGenoDoseFileFromBcftools(
genos.file,
get.coords = TRUE,
get.alleles = TRUE,
use.fread = TRUE,
rm.dup = FALSE,
verbose = 0
)
genos.file |
path to the input file containing the SNP genotype data |
get.coords |
if TRUE, SNP coordinates will also be extracted |
get.alleles |
if TRUE, SNP alleles will also be extracted |
use.fread |
if TRUE, |
rm.dup |
if TRUE, duplicated SNPs (i.e., with the exact same coordinate) will be removed |
verbose |
verbosity level (0/1) |
list with a matrix of SNP genotypes and optional data frames of SNP coordinates and alleles
Timothee Flutre
convertVcfToGenoDoseWithBcftools
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