Question: Convert VCF dosage file into dosage only file
0
gravatar for dp0b
2.1 years ago by
dp0b40
dp0b40 wrote:

Hi,

Is it possibly to only output dosages from a generated vcf dosage file from minimac?

Input format is

##fileformat=VCFv4.1
##filedate=2017.7.5
##source=Minimac3
##contig=<ID=29>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)]">
##INFO=<ID=AF,Number=1,Type=Float,Description="Estimated Alternate Allele Frequency">
##INFO=<ID=MAF,Number=1,Type=Float,Description="Estimated Minor Allele Frequency">
##INFO=<ID=R2,Number=1,Type=Float,Description="Estimated Imputation Accuracy">
##INFO=<ID=ER2,Number=1,Type=Float,Description="Empirical (Leave-One-Out) R-square (available only for genotyped variants)">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  1242658141  1364665948  1242658615
29  11  Chr29:11    A   G   .   PASS    .   GT:DS   0|0:0.193   0|0:0.193   0|0:0.193

Is there an option in vcftools to output the dosages for each genotype seperatly, without the genotype call?

minimac dosage vcf • 2.3k views
ADD COMMENTlink modified 2.1 years ago by trausch1.4k • written 2.1 years ago by dp0b40
3
gravatar for trausch
2.1 years ago by
trausch1.4k
Germany
trausch1.4k wrote:

bcftools query -f "%CHROM\t%POS[\t%DS]" minimac3.dose.vcf.gz

ADD COMMENTlink written 2.1 years ago by trausch1.4k

Missing an \n at the end :):

bcftools query -f "%CHROM\t%POS[\t%DS]\n" minimac3.dose.vcf.gz
ADD REPLYlink written 23 months ago by endrebak790
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1733 users visited in the last hour