Mercurial > repos > greg > coral_multilocus_genotype

changeset 6:0488ca4a8c4e draft

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Uploaded
author greg
date Wed, 11 Nov 2020 18:09:01 +0000
parents 457cbc5ca604
children bcb28b49b0cc
files coral_multilocus_genotype.R
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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");