Question: Vcftools r2 Error: Insufficient sites remained after filtering or No data left for analysis!
5
gravatar for hellbio
3.6 years ago by
hellbio380
hellbio380 wrote:

I am having the below error while calcuating r2 using vcftools:

vcftools --vcf GATK.QC.MAF5.recode.vcf --hap-r2

VCFtools - v0.1.12b
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
--vcf GATK.QC.MAF5.recode.vcf
--max-alleles 2
--min-alleles 2
--hap-r2
--phased

After filtering, kept 133 out of 133 Individuals
Outputting Pairwise LD (phased bi-allelic only)
Error: Insufficient sites remained after filtering

I tried using --geno-r2 --phased and met with the obvious error as the variants are unphased.

vcftools --vcf 133Samples.GATK.QC.MAF5.recode.vcf --geno-r2  --phased

VCFtools - v0.1.12b
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
--vcf 133Samples.GATK.QC.MAF5.recode.vcf
--geno-r2
--max-alleles 2
--min-alleles 2
--phased

After filtering, kept 133 out of 133 Individuals
Outputting genotype pairwise LD (bi-allelic only) for a set of SNPs versus all others.
After filtering, kept 0 out of a possible 9792407 Sites
No data left for analysis!
Run Time = 444.00 seconds

Could anyone comment on how to calculate r2 using vcftools?

r2 ld vcftools • 2.3k views
ADD COMMENTlink modified 3.1 years ago by zhengchenfei60 • written 3.6 years ago by hellbio380

There was a bug in some of these functions in VCFtools 0.1.12. Perhaps a place to start would be to use 0.1.14 (the latest)?

ADD REPLYlink written 3.5 years ago by Brice Sarver3.2k

In my case, I saw that I had a non-phased individual that had been merged with the phased ones and all sites got removed as a result.

ADD REPLYlink written 10 months ago by Gabriel R.2.6k
3
gravatar for zhengchenfei
3.1 years ago by
zhengchenfei60
zhengchenfei60 wrote:

hello, i have this problem too. Did you solve it yet?

ADD COMMENTlink written 3.1 years ago by zhengchenfei60

Did you solve it? I'm facing the same problem.

ADD REPLYlink written 2.5 years ago by mufernando10
1

vcftools --vcf 133Samples.GATK.QC.MAF5.recode.vcf --geno-r2 It's OK --phased is not nessessary

ADD REPLYlink written 21 months ago by zhengchenfei60

its means that the output of that command show the r2 for each SNPs ? and with this information I can delete SNPs with r2 > 0.7?

ADD REPLYlink written 15 days ago by danielpovedam0
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