Commit cd1382aa authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

update module load; platypus update sampleid

parent 420c3786
......@@ -30,8 +30,10 @@ then
fi
baseDir="`dirname \"$0\"`"
source /etc/profile.d/modules.sh
module load igvtools/2.3.71 samtools/1.6
if [[ -z $isdocker ]]
then
source /etc/profile.d/modules.sh
module load igvtools/2.3.71 samtools/1.6
exit
samtools index -@ $NPROC $bam
igvtools count -z 5 $bam ${pair_id}.tdf ${index_path}/igv/human.genome
......@@ -35,9 +35,11 @@ then
NPROC=`nproc`
fi
source /etc/profile.d/modules.sh
module load hisat-genotype/1.0.1
if [[ -z $isdocker ]]
then
source /etc/profile.d/modules.sh
module load hisat-genotype/1.0.1
fi
diff $fq1 $fq2 > difffile
if [ -s difffile ]
......
......@@ -26,8 +26,12 @@ fi
baseDir="`dirname \"$0\"`"
source /etc/profile.d/modules.sh
module load samtools/1.6
if [[ -z $isdocker ]]
then
source /etc/profile.d/modules.sh
module load samtools/1.6
fi
for i in *.bam; do
samtools index -@ $NPROC ${i}
done
......@@ -25,8 +25,10 @@ if [[ -z $NPROC ]]
then
NPROC=`nproc`
fi
source /etc/profile.d/modules.sh
if [[ -z $isdocker ]]
then
source /etc/profile.d/modules.sh
fi
perl $baseDir/concat_cts.pl -o ./ *.cts
perl $baseDir/concat_fpkm.pl -o ./ *.fpkm.txt
perl $baseDir/concat_ctsum.pl -o ./ *.cts.summary
......
......@@ -107,6 +107,12 @@ then
fi
bamlist=`join_by , *.bam`
Platypus.py callVariants --minMapQual=0 --minReads=3 --mergeClusteredVariants=1 --nCPU=$NPROC --bamFiles=${bamlist} --refFile=${reffa} --output=platypus.vcf
for i in *.bam
do
prefix="${i%.bam}"
sid=`samtools view -H ${i} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
perl -pi -e "s/$prefix/$sid/g" platypus.vcf
done
vcf-sort platypus.vcf |vcf-annotate -n --fill-type -n |bgzip > platypus.vcf.gz
tabix platypus.vcf.gz
bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.platypus.vcf.gz platypus.vcf.gz
......
......@@ -24,9 +24,10 @@ function join_by { local IFS="$1"; shift; echo "$*"; }
shift $(($OPTIND -1))
baseDir="`dirname \"$0\"`"
source /etc/profile.d/modules.sh
module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q
if [[ -z $isdocker ]]
source /etc/profile.d/modules.sh
module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q
fi
if [[ -a "${index_path}/genome.fa" ]]
then
reffa="${index_path}/genome.fa"
......
......@@ -190,6 +190,7 @@ then
elif [[ $method == 'itdseek' ]]
then
stexe=`which samtools`
echo $stexe
samtools view -@ $NPROC -L ${itdbed} ${sbam} | itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | java -Xmx30g -jar $SNPEFF_HOME/SnpSift.jar filter "( LEN < 10000 )" | bgzip > ${pair_id}.itdseek.vcf.gz
tabix ${pair_id}.itdseek.vcf.gz
......
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