Commit 80a64aa1 authored by eortega's avatar eortega
Browse files

corrected path management in scripts/04_snpcalling.sh typos correction

parent 3cb49c4a
......@@ -32,7 +32,7 @@ echo $W_seq $R_seq $Other_seq
### CREATE SYMBOLIC LINKS TO SEQUENCE FILES
### DIIVIDED IN 3 DIRECTORIES
### DIVIDED IN 3 DIRECTORIES
echo "CREATE SYMBOLIC LINKS"
......
......@@ -2,21 +2,23 @@
## SNPCALLING
path=$1 ## Working directory's path
path=$1 ## Working directory's path
step_name=$2
bam=$3 ## name of step which created the bam files to be used
ref=$4 ## path to reference.fasta
od=${path}${step_name}/ ## Output directory
prev_step=$3 ## name of step which created the bam files to be used
ref=$4 ## path to reference.fasta
echo ${path}steps/
mkdir -p ${path}steps/
for i in $(find ${path}steps/${bam}/ -type f -name *.bam)
for i in $(find ${path}steps/${prev_step}/ -type f -name *.bam)
do
od2=$(dirname $i);
od2=${od2/mapping/snpcalling}
mkdir -p $od2
od=$(dirname $i)
od=${od/$prev_step/$step_name}
freebayes -b $i -f $ref -C 1 -K -F 0.01 > ${od2}/$(basename -s .sort.bam $i).vcf
mkdir -p $od
freebayes -b $i -f $ref -C 1 -K -F 0.01 > ${od}/$(basename -s .sort.bam $i).vcf;
echo $(basename -s .sort.bam $i).vcf 'has been created';
done
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