From a08836cddcd0092691f4242222e05d2d9078cbab Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 28 Feb 2019 11:43:58 -0600
Subject: [PATCH] hisat genotype reference location bug
---
alignment/hisat_genotype.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/alignment/hisat_genotype.sh b/alignment/hisat_genotype.sh
index 32d5d4d..7e0655e 100644
--- a/alignment/hisat_genotype.sh
+++ b/alignment/hisat_genotype.sh
@@ -41,9 +41,9 @@ diff $fq1 $fq2 > difffile
if [ -s difffile ]
then
-hisatgenotype_extract_reads.py -p 16 --database-list hla --base /project/shared/bicf_workflow_ref/hisat_genotype_hla/genotype_genome -1 $fq1 -2 $fq2 --out-dir hisatgeno_out
+hisatgenotype_extract_reads.py -p 16 --database-list hla --base /project/shared/bicf_workflow_ref/human/hisat_genotype_hla/genotype_genome -1 $fq1 -2 $fq2 --out-dir hisatgeno_out
else
-hisatgenotype_extract_reads.py -p 16 --database-list hla --base /project/shared/bicf_workflow_ref/hisat_genotype_hla/genotype_genome -U $fq1 --out-dir hisatgeno_out
+hisatgenotype_extract_reads.py -p 16 --database-list hla --base /project/shared/bicf_workflow_ref/human/hisat_genotype_hla/genotype_genome -U $fq1 --out-dir hisatgeno_out
fi
hisatgenotype_locus_samples.py -p 16 --region-list hla.A,hla.B,hla.C,hla.DQA1,hla.DQB1,hla.DRB1,hla.DPB1 --assembly --read-dir hisatgeno_out --out-dir ${pair_id}.hisat_hla > ${pair_id}.hisat_hla.txt
--
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