Convert vcf phased data to plink

Question

[NB]

I have a phased haplotype format vcf file that looks like this

##fileformat=VCFv4.0
##reference=human_b36_both.fasta
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA12891 NA12892 NA12878 NA19239 NA19238 NA19240
22      47812545        rs5769818       A       G       .       PASS    GT      0|1     0|1     0|1     1|1     1|1     1|1
22      47812939        rs9616222       A       G       .       PASS    GT      0|1     0|1     0|1     1|0     1|1     1|1
22      47813002        rs5769819       A       G       .       PASS    GT      0|1     0|1     0|1     1|0     1|1     1|1
22      47813051        rs5769820       G       A       .       PASS    GT      1|0     1|0     1|0     1|0     1|1     1|1
22      47813163        rs5769821       A       G       .       PASS    GT      0|1     0|1     0|1     1|0     1|1     1|1

I do not have additional files or ped files to this.

I would like to calculate the identity by state (IBS) between all pairs of individuals - is there a way to convert this file into plink format or are there any tools that can take in vcf to calculate IBS ?

Thank you

Answer 1

[Gabriel R.]

You can try glactools, it is just one line:

glactools vcfm2acf --onlyGT  --fai /Data/reference/human_g1k_v37.fasta.fai  /tmp/biostars/test.vcf  | glactools acf2bplink - /tmp/biostars/test

You need to edit the genetic distance in the bim file and probably the fam files as well.

Answer 2

[Kevin Blighe]

Yes, PLINK can read VCFs: https://www.cog-genomics.org/plink/1.9/input#vcf

You may want to check some of the other parameters that can be used when converting, such as:

• --keep-allele-order
• --vcf-idspace-to
• --const-fid
• --allow-extra-chr
• --split-x

Kevin

[NB]

thanks Kevin, I try to do that but end up wit a file that has 0 for each individual.

[Kevin Blighe]

Any log or error messages?

[NB]

No, so this is what I did (playing around with a chunk of chr22)

##convert vcf to plink
./plink --vcf input_genotype.vcf --keep-allele-order  --allow-extra-chr 0 --make-bed --out MyData

##tried to calculate IBS using King
/king -b MyData.bed --ibs

The result from above is an empty file

Then I tried to convert bim bam bed to map and ped

./plink --bfile MyData --recode --tab --out test

The ped file is just 0

NA12891 NA12891 0       0       0       -9      0 0     0 0     0 0     0 0     0 0

[Kevin Blighe]

If you avoid using --make-bed and instead produce a plain text PLINK dataset, can you then see data in that?

[NB]

still the same. I don't think PLINK can handle phased Haplotype file in the format 0|1, where 0 indicates ref and 1 is for the alt allele. Can it ?

[Kevin Blighe]

It can handle phased, as I show in Step 5, here: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2 (the 1000 Genomes data is all phased). I will move my answer back to a comment. Perhaps the PLINK developer will pick it up later (in different time zone).

[NB]

Ah, for now, I was able to sort my issue out using the R package SNPrelate. It takes in the vcf file as input, calculates IBS and then if one feels like it, it can also convert it to PLINK format !