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Commit 9975bc74 authored by Brandi Cantarel's avatar Brandi Cantarel
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add reference genome

parent a0f3cd94
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variants/norm_annot.sh
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...@@ -15,6 +15,7 @@ do ...@@ -15,6 +15,7 @@ do
case $opt in case $opt in
p) pair_id=$OPTARG;; p) pair_id=$OPTARG;;
v) vcf=$OPTARG;; v) vcf=$OPTARG;;
r) index_path=$OPTARG;;
h) usage;; h) usage;;
esac esac
done done
...@@ -25,6 +26,15 @@ baseDir="`dirname \"$0\"`" ...@@ -25,6 +26,15 @@ baseDir="`dirname \"$0\"`"
source /etc/profile.d/modules.sh source /etc/profile.d/modules.sh
module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q
if [[ -a "${index_path}/genome.fa" ]]
then
reffa="${index_path}/genome.fa"
dict="${index_path}/genome.dict"
else
echo "Missing Fasta File: ${index_path}/genome.fa"
usage
fi
perl $baseDir\/uniform_vcf_gt.pl $pair_id $vcf perl $baseDir\/uniform_vcf_gt.pl $pair_id $vcf
bgzip -f ${pair_id}.uniform.vcf bgzip -f ${pair_id}.uniform.vcf
......
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