CODEWITHSUNDEEP
rbioinformaticsvcf-variant-call-format
Victor.H
Victor.H

Reputation: 157

Convert vcf to hap file, collapse genotypes

I use photos to ask a question.

I want my output file only have number/line/sample.

How can I remove newdata...C...and ""

Any suggestions?

Note: I am the first time to ask a question in here. I am try to follow the rules. I am still studying.

Upvotes: 0

Views: 410

Answers (1)

zx8754
zx8754

Reputation: 56219

Try this example:

library(data.table)

# example vcf
hap <- fread('
##fileformat=VCFv4.0
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA00001 NA00002 NA00003
19  111 .   A   C   9.6 .   .   GT  0|0 0|0 0|1
19  112 .   A   G   10  .   .   GT  0|0 1|0 1|1
19  112 .   A   G   4   .   .   GT  1|0 1|0 1|1
')

data.table(gsub("|", "", do.call(paste0, hap[, -c(1:9)]), fixed = TRUE))
#        V1
# 1: 000001
# 2: 001011
# 3: 101011

Upvotes: 2

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