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Vcftools r2 Error: Insufficient sites remained after filtering or No data left for analysis!

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?

vcftools r2 ld
• 7,127 views • link
updated by Chenfei Zheng Chenfei Zheng • written by hellbio hellbio

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)?

• 0 views • link
written by Brice Sarver Brice Sarver

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.

• 1 views • link
written by Gabriel R. Gabriel R.

1 answer

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

• 0 views • link
written by Chenfei Zheng Chenfei Zheng

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

• 0 views • link
written by mufernando • mufernando

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

• 0 views • link
written by Chenfei Zheng Chenfei Zheng

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?

• 0 views • link
written by danielpovedam • danielpovedam

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