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lpoecklpoeck
authoredJun 17, 2019
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‎bdmax/bdmax.sh

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#!/bin/bash
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#Usage: bdmax.sh <bamfile> <output directory> <cutoff value> <calculate_lower>
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#example : ./bdmax.sh lumpy_BSY_red.bam output_bdmax 60 3
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#cutoff = 60
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#calculate_lower should be 3 for BSY10dKU70 and 2 for BSY11dKU70 (only the full version works with breakdancer)
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bamfile="$1"
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cutoff=41
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stamp="$5"
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output="$6"
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conf="bdmaxconfig"
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cd ..
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if [[ $1 == *"BSY11"* ]]
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then
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c=2
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else
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c=3
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fi
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if [[ $1 == *"BSY11_red"* ]]
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then
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conf="BSY11_red_config"
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else
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docker run --name=bdmax1 -v $(pwd):/in/ -w /in/ molecular/breakdancer perl ../home/bio/breakdancer-1.4.5/perl/bam2cfg.pl -c "$c" "$bamfile".bam > ./bdmax/bdmaxconfig
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fi
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START=$(docker inspect --format='{{.State.StartedAt}}' bdmax1)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' bdmax1)
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START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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TIME1=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo first time: $TIME1 seconds
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docker container rm bdmax1
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echo $conf
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docker run --name=bdmax2 -v $(pwd):/in/ -w /in/ molecular/breakdancer breakdancer-max -y $cutoff ./bdmax/"$conf" > "$output"/bdmax/bdmax_"$stamp".vcf
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START=$(docker inspect --format='{{.State.StartedAt}}' bdmax2)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' bdmax2)
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START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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TIME2=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo second time: $TIME2 secondssss
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FTIME=$(($TIME1+$TIME2))
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echo final time: $FTIME seconds 2>&1 | tee "$output"/bdmax/bdmax_runtime_"$stamp".txt
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docker container rm bdmax2
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‎breseq/breseq.sh

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#!/bin/bash
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bam="$1"
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fasta="$2"
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fastq1="$3"
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fastq2="$4"
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stamp="$5"
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output="$6"
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cd ..
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docker run --name=breseq -v $(pwd)/:/in/ -w /in/ pvstodghill/breseq:0.32.0__2018-03-15 breseq -o "$output"/breseq/breseq_output_"$stamp" -r "$fasta".fasta "$fastq1".fastq "$fastq2".fastq
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START=$(docker inspect --format='{{.State.StartedAt}}' breseq)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' breseq)
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START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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FTIME=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo final time: $FTIME seconds 2>&1 | tee "$output"/breseq_runtime_"$stamp".txt
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docker container rm breseq

‎delly/delly.sh

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#!/bin/bash
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bam="$1"
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fasta="$2"
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fastq1="$3"
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fastq2="$4"
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stamp="$5"
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output="$6"
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cd ..
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docker run --name=delly -v $(pwd)/:/in/ -w /in/ dellytools/delly delly call -o "$output"/delly/delly_output_"$stamp".vcf -g "$fasta".fasta "$bam".bam
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START=$(docker inspect --format='{{.State.StartedAt}}' delly)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' delly)
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START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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TIME1=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo first time: "$TIME1"
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docker container rm delly
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docker run --name=bcftools -v $(pwd)/delly/output/:/in/ -w /in/ halllab/bcftools:v1.9 bcftools view -i'FILTER="PASS" && MAPQ>40 && (PE>5 || SR>5)' delly_output_"$stamp".vcf > ./delly/output/delly_output_BCFTOOLS_"$stamp".vcf.vcf
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START=$(docker inspect --format='{{.State.StartedAt}}' bcftools)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' bcftools)
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START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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TIME2=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo seocnd time: "$TIME2"
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docker container rm bcftools
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FTIME=$(($TIME1+$TIME2))
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echo final time: $FTIME seconds 2>&1 | tee "$output"/delly/delly_runtime_"$stamp".txt

‎doall.sh

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#!/bin/bash
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#tests all tools with all alignments we had deemed necessary
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#usage: ./doall.sh <output name>
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#example: ./doall.sh newoutput
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# creates a directory called "newoutput" that contains the results of all four alignments for each tool
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#if no outputn name is provided, a timestamp is used as a default
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echo "calling tools with predeterminded parameters"
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declare -a params=("BSY10_red"
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"BSY11_red"
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"BSY10_full"
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"BSY11_full")
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stamp="$(date +'%Y_%m_%d-%H_%M_%S')"
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oname="$1"
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if [ -z "$1" ]
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then
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echo "No name supplied, setting time stamp as default"
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oname="$stamp"
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fi
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mkdir output_"$oname"
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mkdir output_"$oname"/BSY11
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mkdir output_"$oname"/BSY11/red
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mkdir output_"$oname"/BSY11/full
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mkdir output_"$oname"/BSY10
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mkdir output_"$oname"/BSY10/red
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mkdir output_"$oname"/BSY10/full
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declare -a tools=("bdmax" "delly" "gridss" "lumpy" "manta" "softsv" "breseq" "metasv")
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for tool in "${tools[@]}"
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do
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mkdir output_"$oname"/BSY11/red/"$tool"
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mkdir output_"$oname"/BSY11/full/"$tool"
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mkdir output_"$oname"/BSY10/red/"$tool"
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mkdir output_"$oname"/BSY10/full/"$tool"
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done
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ref="reference/cbs_7435_full"
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for p in "${params[@]}"
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do
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echo "calling with $p"
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if [[ $p == *"BSY11"* ]]
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then
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if [[ $p == *"_red"* ]]; then
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output=output_"$oname"/BSY11/red
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bam="BSY11/BSY11_red"
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fastq1="BSY11/BSY11_1_trimmed_red"
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fastq2="BSY11/BSY11_2_trimmed_red"
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else
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output=output_"$oname"/BSY11/full
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bam="BSY11/BSY11_full"
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fastq1="BSY11/BSY11_1_trimmed"
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fastq2="BSY11/BSY11_2_trimmed"
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fi
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else
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if [[ $p == *"_red"* ]]; then
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output=output_"$oname"/BSY10/red
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bam="BSY10/BSY10_red"
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fastq1="BSY10/BSY10_1_trimmed_red"
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fastq2="BSY10/BSY10_2_trimmed_red"
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else
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output=output_"$oname"/BSY10/full
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bam="BSY10/BSY10_full"
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fastq1="BSY10/BSY10_1_trimmed"
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fastq2="BSY10/BSY10_2_trimmed"
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fi
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fi
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bash ./doit.sh "$bam" "$ref" "$fastq1" "$fastq2" "$oname" "$output" 2>&1
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done
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echo "doall done, fingers crossed"

‎doit.sh

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#!/bin/bash
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#tests all tools usings a single alignment
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#usage: ./doit.sh <bamfile name> <reference file name> <fastq1 file name> <fastq2 file name> <output name> <output folder>
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# all file names are provided WITHOUT FILE EXTENSION
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#example: ./doit.sh BSY11_trimmed_red cbs_7435_full 100549_1_trimmed 100549_2_trimmed test1 testoutput
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echo "testing all tools..."
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docker kill $(docker ps -q)
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docker rm $(docker ps -a -q)
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declare -a tools=("bdmax" "delly" "gridss" "lumpy" "manta" "softsv" "breseq")
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#("bdmax" "breseq" "delly" "gridss" "lumpy" "manta" "metasv" "softsv")
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dir="$(pwd)"
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for tool in "${tools[@]}"
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do
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stamp="$(date +'%Y_%d_%m-%H_%M_%S')"
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echo "╔══════════════════════════════════════════════════════════════╗"
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echo "║ starting $tool ║"
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echo "╚══════════════════════════════════════════════════════════════╝"
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cd "$dir"/"$tool"
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./$tool.sh "$1" "$2" "$3" "$4" "$5" "$6" 2>&1 | tee ../"$6"/"$tool"/"$tool"_out_"$5".txt
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echo "##################### DONE WITH $tool ######################"
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done
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echo "That's all, folks!"

‎gridss/gridss.sh

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#!/bin/bash
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stamp="$5"
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bam="$1"
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fasta="$2"
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fastq1="$3"
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fastq2="$4"
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output="$6"
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cd ..
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mkdir "$output"/gridss/gridss_out_"$stamp"
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docker run --name=gridss -v $(pwd)/:/in/ -w /in/ gridss/gridss OUTPUT="$output"/gridss/gridss_out_"$stamp"/output_file_"$stamp".vcf INPUT="$bam".bam REFERENCE_SEQUENCE="$fasta".fasta ASSEMBLY="$output"/gridss/gridss_out_"$stamp"/output_file_"$stamp".bam
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START=$(docker inspect --format='{{.State.StartedAt}}' gridss)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' gridss)
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START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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FTIME=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo final time: $FTIME seconds 2>&1 | tee "$output"/gridss/gridss_runtime_"$stamp".txt
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docker container rm gridss

‎lumpy/lumpy.sh

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#!/bin/bash
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stamp="$5"
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output="$6"
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cd ..
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docker run --name=lumpy -v $(pwd)/:/in/ -w /in/ erictdawson/lumpy-sv lumpyexpress -B "$1".bam -S "$1".splitters.bam -D "$1".discordants.bam -o "$output"/lumpy/lumpyoutput_"$stamp".vcf
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./lumpy/lumpy_awk_filter.sh "$output"/lumpy/lumpyoutput_"$stamp".vcf 100 "$output"/lumpy/lumpyoutput_CUTOFF_"$stamp".vcf
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#rm ./lumpy/output/lumpyoutput_"$stamp".vcf
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START=$(docker inspect --format='{{.State.StartedAt}}' lumpy)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' lumpy)
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START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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FTIME=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo final time: $FTIME seconds 2>&1 | tee "$output"/lumpy/lumpy_runtime_"$stamp".txt
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docker container rm lumpy

‎lumpy/lumpy_awk_filter.sh

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#!/bin/bash
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#
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# Usage:
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# awk_filter.sh <filename> <cutoff value> <output filename>
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#
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# Examples:
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# lumpy_awk_filter.sh example.vcf 100 cutoff.vcf
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#
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if [ $# -lt 2 ]; then
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echo -e "Usage:\n `basename ${0}` <filename> <cutoff value> <output filename>"
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exit 1
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fi
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fname=${1}
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cutoff=${2}
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output=${3}
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odir="."
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awk -v cutoff=${cutoff} -F ";" -e \
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'{
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for (i=1;i<=NF;i++) {
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if ($i ~ /SU=/) {
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tmp=match($i, /[0-9]/);
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if ((substr(($i),tmp))+0 > cutoff) {
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print($0);
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}
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}
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}
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}' ${fname} > ${output}

‎manta/manta.sh

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# Usage: manta.sh <bamfile> <reference fasta> <output directory> <number of available cores>
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#
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bam="$1"
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fasta="$2"
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fastq1="$3"
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fastq2="$4"
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cores=1
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stamp="$5"
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output="$6"
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cd ..
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docker run --name=manta1 -v $(pwd):/in/ -w /in/ kfdrc/manta ../manta-1.4.0.centos6_x86_64/bin/configManta.py --bam="$bam".bam --referenceFasta="$fasta".fasta --runDir="$output"/manta/output_"$stamp"
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15+
START=$(docker inspect --format='{{.State.StartedAt}}' manta1)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' manta1)
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18+
START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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TIME1=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo first time: $TIME1 seconds
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docker container rm manta1
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docker run --name=manta2 -v $(pwd):/in/ -w /in/ kfdrc/manta python "$output"/manta/output_"$stamp"/runWorkflow.py -m local -j $cores
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START=$(docker inspect --format='{{.State.StartedAt}}' manta2)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' manta2)
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33+
START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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TIME2=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo second time: $TIME2 seconds
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docker container rm manta2
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FTIME=$(($TIME1+$TIME2))
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echo final time: $FTIME seconds 2>&1 | tee "$output"/manta/manta_runtime_"$stamp".txt

‎mapping.sh

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#!/bin/bash -x
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#Shell script for mapping procedure
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#Lea Demelius - 20.2.2019
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echo "Starting mapping procedure..."
5+
fasta="$1"
6+
fastq1="$2"
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fastq2="$3"
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name="$4"
9+
docker pull lindsayliang/bwa_mem
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docker pull kfdrc/speedseq
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docker pull rpseq/samblaster
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docker pull jweinstk/samtools
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docker pull erictdawson/lumpy-sv
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docker run --rm -v $(pwd):/in/ -w /in/ lindsayliang/bwa_mem bwa index $fasta
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docker run --rm -v $(pwd):/in/ -w /in/ lindsayliang/bwa_mem bwa mem -R "@RG\tID:id\tSM:100549\tLB:lib" $fasta $fastq1 $fastq2 > x.sam
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docker run --rm -v $(pwd):/in/ -w /in/ rpseq/samblaster -i x.sam --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 > y.sam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools view -S -b y.sam > z.unsorted.bam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools sort z.unsorted.bam -o $name.bam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools view -b -F 1294 $name.bam > z.discordants.unsorted.bam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools view -h $name.bam > z.splitters.before.bam
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docker run --rm -v $(pwd):/in/ -w /in/ erictdawson/lumpy-sv ../app/lumpy-sv/scripts/extractSplitReads_BwaMem -i z.splitters.before.bam > z.splitters.nearlythere.sam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools view -Sb z.splitters.nearlythere.sam > z.splitters.unsorted.bam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools sort z.discordants.unsorted.bam -o $name.discordants.bam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools sort z.splitters.unsorted.bam -o $name.splitters.bam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools index $name.bam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools index $name.discordants.bam
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docker run --rm -v $(pwd):/in/ -w /in/ jweinstk/samtools samtools index $name.splitters.bam
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rm z.splitters.unsorted.bam
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rm z.discordants.unsorted.bam
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rm z.splitters.nearlythere.sam
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rm z.splitters.before.bam
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rm z.unsorted.bam
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rm y.sam
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rm x.sam
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echo "End of mapping procedure"

‎softsv/softsv.sh

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#!/bin/bash
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stamp="$5"
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bam="$1"
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fasta="$2"
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fastq1="$3"
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fastq2="$4"
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output="$6"
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cd ..
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mkdir "$output"/softsv/softsv_output_"$stamp"
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docker run --name=softsv -v $(pwd)/:/in/ -w /in/ chrishah/softsv:1.4.2 SoftSV -i "$bam".bam -o "$output"/softsv/softsv_output_"$stamp"
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./softsv/softsv_awk_filter.sh "$output"/softsv/softsv_output_"$stamp" 100
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START=$(docker inspect --format='{{.State.StartedAt}}' softsv)
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STOP=$(docker inspect --format='{{.State.FinishedAt}}' softsv)
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17+
START_TIMESTAMP=$(date --date=$START +%s)
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STOP_TIMESTAMP=$(date --date=$STOP +%s)
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20+
TIME1=$(($STOP_TIMESTAMP-$START_TIMESTAMP))
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echo final time: $TIME1 seconds 2>&1 | tee "$output"/softsv/softsv_runtime_"$stamp".txt
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docker container rm softsv

‎softsv/softsv_awk_filter.sh

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#!/bin/bash
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#
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# Usage:
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# softsv_awk_filter.sh <directoryname> <cutoff value>
5+
#
6+
# Examples:
7+
# softsv_awk_filter.sh softsv_directory 100
8+
#
9+
10+
if [ $# -lt 2 ]; then
11+
echo -e "Usage:\n `basename ${0}` <directoryname> <cutoff value>"
12+
exit 1
13+
fi
14+
15+
dname=${1}
16+
cutoff=${2}
17+
odir="."
18+
19+
for file in ${dname}/*.txt ; do
20+
awk -v cutoff=${cutoff} -F " " -e \
21+
'{
22+
if ($5+$6 > cutoff) {
23+
print $0;
24+
}
25+
}' $file > $file'_cutoff.txt';
26+
done

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