I am trying to manipulate my vcf and writing new vcf subsets but after the vcf is read, I am unable to write or change the format to .bed. However, I do not see any problem with the format.
format(snp)
"<S4 class ‘vcfR’ [package “vcfR”] with 3 slots>"
Object of Class vcfR
288 samples
40743 CHROMs
239,286 variants
Object size: 1279.8 Mb
0 percent missing data
write.vcf(snp, "snp.vcf")
WRITING VCF
This is not a vcf!
Error in write.vcf(snp, "snp.vcf")
I am trying to manipulate my vcf and writing new vcf subsets but after the vcf is read, I am unable to write or change the format to .bed. However, I do not see any problem with the format.
format(snp) "<S4 class ‘vcfR’ [package “vcfR”] with 3 slots>"
Object of Class vcfR 288 samples 40743 CHROMs 239,286 variants Object size: 1279.8 Mb 0 percent missing data
write.vcf(snp, "snp.vcf") WRITING VCF