VCFtools. Get rid of DS:GP phased genotypes while keeping GT and remaining fields

Question

[Mr Locuace]

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

Answer 1

[cpad0112]

Good description of requirements. It would help if you could post some example input data. try, to retain only GT from format field:

 bcftools annotate -x ^FORMAT/GT test.vcf

ps: could you please edit the title replacing read of with rid of

[finswimmer]

@ 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

[cpad0112]

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

Answer 2

[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