Admixture error in removing loci with no genotypes even after filtering loci
0
0
Entering edit mode
11 months ago
Whirlingdaf ▴ 40

I am attempting to run ADMIXTURE on plink derived .bed files and continue to get the error

Error: detected that all genotypes are missing for a SNP locus.
Please apply quality-control filters to remove such loci.

I have already performed multiple quality control steps prior to this point. E.g:

Filtered my vcf to: keep variants that have been successfully genotyped in 20% of individuals, a minimum quality score of 10, and a minor allele count of 3

vcftools --gzvcf bcftools_merged.vcf.gz --max-missing 0.2 --mac 3 --minQ 10 --recode --recode-INFO-all --out bcftools_filtered

Apply a minimum depth for genotypes:

vcftools --vcf bcftools_filtered.vcf --minDP 10 --recode --recode-INFO-all --out bcftools_filtered2

Then work with plink to create bed files and filter for LD as recommended in the tutorial:

plink --vcf bcftools_filtered2.vcf --make-bed --out bcftools_filtered2 --allow-extra-chr --chr-set 38
plink --bfile bcftools_filtered2 --indep-pairwise 50 10 0.1 --allow-extra-chr --chr-set 38
plink --bfile bcftools_filtered2 --extract plink.prune.in --make-bed --out prunedData --allow-extra-chr --chr-set 38

As I also have a number of non-numeric scaffolds, I need to remove these before running ADMIXTURE:

awk '{$1="0";print $0}' prunedData.bim > prunedData.bim.tmp
mv prunedData.bim.tmp prunedData.bim

And finally, attempt to run Admixture:

for K in 2 3 4 5 6 7 8 9 10; do admixture --cv prunedData.bed $K -j6 | tee log${K}.out; done

Which still returns the error:

Cross-validation will be performed.  Folds=5.
Parallel execution requested.  Will use 6 threads.
Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
Error: detected that all genotypes are missing for a SNP locus.
Please apply quality-control filters to remove such loci.

I would truly appreciate any assistance, I am running out of ideas to trouble shoot this.

Thank you!

plink ADMIXTURE vcftools • 489 views
ADD COMMENT

Login before adding your answer.

Traffic: 2605 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6