Question: impute2 output files to vcf
0
gravatar for tarek.mohamed
6 weeks ago by
tarek.mohamed260
tarek.mohamed260 wrote:

Hi All,

I need to know how can I deal with impute2 output file, how can I convert them to vcf files or is there a way by which I get vcf files as an impute2 output

I has a vcf file with a gwas dataset for which I need to run impute2.

I converted the vcf file into plink (bed,bim,fam) fromat, then I phased these files using shapit. Shapeit returned two files (.hap and .sample).

I imputed .hap and .sample files with the reference panel files using inpute2

$ impute2 -use_prephased_g -known_haps_g snps_omni_6samples.phased.refpanel.haps \
        snps_omni_6samples.phased.refpanel.sample \
        -h ALL.chr9.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.nosing.haplotypes.gz \
        -l ALL.chr9.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.nosing.legend.gz \
        -m genetic_map_chr9_combined_b37.txt \
        -int 86890852 86983368 \
        -Ne 20000 \
        -o snps.omni.6samples_imputed

Impute2 returned

$ cat snps.omni.6samples_imputed | head -n5              
--- rs45529242 86890852 A T 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
--- rs11140489 86890931 T A 0 1 0 1 0 0 1 0 0 0 1 0 0 1 0 1 0 0
--- rs182458878 86890954 C A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
--- rs187090359 86890989 A G 0.995 0.005 0 1 0 0 0.995 0.005 0 0.995 0.005 0 0.995 0.005 0 0.995 0.005 0
--- rs139866310 86891235 A AAATT 0.021 0.971 0.008 1 0 0 0.992 0.008 0 0 0.992 0.008 0 0.992 0.008 0.992 0.008 0

and

$ cat snps.omni.6samples_imputed_info | head -n5
snp_id rs_id position a0 a1 exp_freq_a1 info certainty type info_type0 concord_type0 r2_type0
--- rs45529242 86890852 A T 0.000 0.000 1.000 0 -1 -1 -1
--- rs11140489 86890931 T A 0.250 1.000 1.000 0 -1 -1 -1
--- rs182458878 86890954 C A 0.000 -0.000 1.000 0 -1 -1 -1
--- rs187090359 86890989 A G 0.002 0.003 0.995 0 -1 -1 -1

and

$ cat snps.omni.6samples_imputed_info_by_sample | head -n5 concord_type0 r2_type0
1.000 1.000
0.989 0.983
0.968 0.873
1.000 1.000
output vcf file impute2 • 192 views
ADD COMMENTlink modified 6 weeks ago by RamRS25k • written 6 weeks ago by tarek.mohamed260
1

For now, the most efficient way to do this depends on what information you need in the VCF. Do you just need high-likelihood genotype calls (VCF "GT" field), or dosage values ("DS" field), or raw posterior-probability triplets ("GP" field)? And what phase information, if any, do you want to keep?

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by chrchang5236.3k

I was able to get the genotypes as follows, re-ran impute2 with flag -phase to generate haplotypes file. Then I used shapeit to convert get vcf files

shapeit -convert --input-haps impute2 --output-vcf impute2.vcf

How can I keep the raw posterior-probability triplets in the .gen file ("GP")??

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by tarek.mohamed260
1

Unfortunately, I'm not sure there's any preexisting program that'll integrate everything for you; there isn't even a real standard for simultaneously representing genotype-likelihood and phase information in VCF files yet. (I use the HDS field defined by Minimac4 in my own work, but that only addresses the smaller dosage + phase problem.) You might need to write something yourself. qctool2 may be worth trying, though.

ADD REPLYlink written 6 weeks ago by chrchang5236.3k
1
gravatar for zx8754
6 weeks ago by
zx87548.9k
London
zx87548.9k wrote:

Possible duplicate:

ADD COMMENTlink written 6 weeks ago by zx87548.9k

My impute2 file has a different identifier than what is required by bcftools to work (CHROM:POS_REF_ALT).

ADD REPLYlink written 6 weeks ago by tarek.mohamed260

You can use SHAPEIT to convert IMPUTE2 GEN format to VCF.

QCTOOL also does it, but will not retain phasing information.

Also, MEGA2: A: How to convert IMPUTE2 to VCF format

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Kevin Blighe53k

How can I convert it using shapeit. I did not see that Gen format is an input option in shapeit convert? Thanks

ADD REPLYlink written 6 weeks ago by tarek.mohamed260

Does this work?

shapeit -convert \
  --input-gen gwas \
  --output-vcf gwas.vcf
ADD REPLYlink written 6 weeks ago by Kevin Blighe53k
1

I re-ran impute2 with flag -phase to generate haplotypes file. Then I used shapeit to convert get vcf files

shapeit -convert --input-haps impute2 --output-vcf impute2.vcf
ADD REPLYlink written 6 weeks ago by tarek.mohamed260
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: 1719 users visited in the last hour