Page Comparison

ssh user123@o2.hms.harvard.edu

# set up screen software: https://wiki.rc.hms.harvard.edu/pages/viewpage.action?pageId=20676715
cp /n/shared_db/misc/rcbio/data/screenrc.template.txt ~/.screenrc

screen  # start screen session. For detail: https://wiki.rc.hms.harvard.edu/pages/viewpage.action?pageId=20676715

srun --pty -p interactive -t 0-12:0:0 --mem 16000MB -n 2 /bin/bash

mkdir /n/scratch3/users/${USER:0:1}/$USER/testGATK4
cd /n/scratch3/users/${USER:0:1}/$USER/testGATK4

# This will setup the path and environmental variables for the pipeline
module load gcc/6.2.0 python/2.7.12 java/jdk-1.8u112 star/2.5.4a
export PATH=/n/shared_db/singularity/hmsrc-gatk/bin:/home/ld32/rcbioDev/bin:$PATH

# setup database. Only need run this once. It will setup database in home, so make sure you have at least 5G free space at home.
setupDB.sh

cp /n/shared_db/singularity/hmsrc-gatk/scripts/* .
buildSampleFoldersFromSampleSheet.py sampleSheet.xlsx

less fastqToBamGermline.sh

# Here is the content of fastqToBamGermline.sh
#!/bin/sh

module load gcc/6.2.0 python/2.7.12 java/jdk-1.8u112 samtools/1.9 bwa/0.7.17

[ -d group2 ] || { echo group2 is not found. You need at least two groups to run this pipeline; exit 1; }

pwdhere=`pwd`

for group in `ls -d group*/|sed 's|[/]||g'`; do
    echo working on group:  $group
    cd $pwdhere/$group
    inputsams=""
	for sample in `ls -d */|sed 's|[/]||g'`; do
        rm $pwdhere/unmappedBams/$group/$sample.inputBamList.txt 2>/dev/null
        mkdir -p $pwdhere/unmappedBams/$group/$sample
        echo working on sample: $sample
        
for r1 in `ls $sample/*_1.fastq $sample/*_1.fq 2>/dev/null`; do
            readgroup=${r1#*/}
            readgroup=${readgroup%_*}
            r2=${r1%_*}_2${r1##*_1}
            echo working on readgroup: $readgroup
                        [[ -f $r2 ]] || { echo -e "\n\n!!!Warning: read2 file '$r2' not exist, ignore this warning if you are working with single-end data\n\n"; r2=""; }

            #@1,0,fastqToSam,,sbatch -p short -t 0-4 --mem 4G
            java -XX:+UseSerialGC -Xmx8G -jar /n/app/picard/2.8.0/bin/picard-2.8.0.jar FastqToSam \
               	FASTQ=$r1 \
                FASTQ2=$r2 \
                OUTPUT=$pwdhere/unmappedBams/$group/$sample/$readgroup.bam \
                READ_GROUP_NAME=${readgroup##*_} \
                SAMPLE_NAME=$sample \
                LIBRARY_NAME=${readgroup%%_*} \
                PLATFORM_UNIT=H0164ALXX140820.2 \
                PLATFORM=illumina \
                SEQUENCING_CENTER=BI \
                RUN_DATE=2014-08-20T00:00:00-0400
                
			inputsams="$inputsams INPUT=$pwdhere/unmappedBams/$group/$sample/$readgroup.bam"	
        done
        sed "s/inputBamFileNamePath/${pwdhere//\//\\/}\/unmappedBams\/$group\/$sample.bam/" $pwdhere/gatk4-rna-germline-variant-calling.inputs.template.json  > $pwdhere/unmappedBams/$group/$sample.json
        #@2,1,merge,,sbatch -p short -n 1 -t 0-4:0 --mem 12G
        java -Xmx12g -jar $PICARD/picard-2.8.0.jar MergeSamFiles VALIDATION_STRINGENCY=SILENT OUTPUT=$pwdhere/unmappedBams/$group/$sample.bam  $inputsams SORT_ORDER=coordinate && samtools index $pwdhere/unmappedBams/$group/$sample.bam
    done
done