Hello, I have a question about VCFtools
I have a vcf file with the usual 9 columns in addition to phased data of several samples. The phased data is in this format: GT:DS:GP (e.g., 0|0:0:1,0,0). I would like to get the original vcf file but only with the GT genotypes (0|0).
With the VCFtools (v0.1.14) command "--extract-FORMAT-info GT" I get the GT genotypes but only CHROM and POS columns.
If someone knows how to do this with this or another software it would be very helpful. Thank you
@ cpad0112 you should move it to an answer.
And this time I can show you how to do this (a bit) shorter :) :
$ bcftools annotate -x 'FORMAT' test.vcf
From the manual:
Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT
You had me there @ finswimmer ...but let me shorten it further:
$ bcftools annotate -x 'fmt' test.vcf
btw, thanks for the bcftools trick/tip. finswimmer
If awk is also fineyou can do it like this:
$ awk -v FS="\t" -v OFS="\t" '{for(i=9;i<=NF;i++) {split($i, gt, ":"); $i=gt[1]} print}' input.vcf > output.vcf
In each column from the FORMAT column until the end, awk splits the values in the column by : and replaces the old column value with only the first resulted value after splitting (which should be the genotype or GT in the FORMAT column).
fin swimmer
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