Mercurial > repos > greg > coral_multilocus_genotype
diff coral_multilocus_genotype.R @ 6:0488ca4a8c4e draft
Uploaded
author | greg |
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date | Wed, 11 Nov 2020 18:09:01 +0000 |
parents | 34e02e8b4232 |
children | bcb28b49b0cc |
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--- a/coral_multilocus_genotype.R Wed Nov 11 18:08:10 2020 +0000 +++ b/coral_multilocus_genotype.R Wed Nov 11 18:09:01 2020 +0000 @@ -418,8 +418,8 @@ # Subset VCF to the user samples. start_time <- time_start("Subsetting vcf to the user samples"); -l <- length(i) + 1; -svcf <- vcf[, 1:l]; +affy_list <- append(stag_db_report$affy_id,"FORMAT"); +svcf <- vcf[,colnames(vcf@gt) %in% affy_list]; write.vcf(svcf, "subset.vcf.gz"); vcf.fn <- "subset.vcf.gz"; snpgdsVCF2GDS(vcf.fn, "test3.gds", method="biallelic.only");