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Replace bwa with bwa-mem2 #50

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Replace bwa with bwa-mem2 #50

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1241ff5
move to bwa-mem2
nr23730 Nov 11, 2021
f431740
auto generate bwa-mem2 index
nr23730 Feb 28, 2022
b72b6f6
Merge branch 'beta_test' into HEAD
nr23730 Feb 28, 2022
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3 changes: 0 additions & 3 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,9 +1,6 @@
[submodule "tools/FastQC"]
path = tools/FastQC
url = https://github.com/s-andrews/FastQC
[submodule "tools/bwa"]
path = tools/bwa
url = https://github.com/lh3/bwa.git
[submodule "tools/bam-readcount"]
path = tools/bam-readcount
url = https://github.com/genome/bam-readcount
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2 changes: 1 addition & 1 deletion RScripts/Report.Rnw
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Expand Up @@ -559,7 +559,7 @@ if(dim(germ_all$muts_tab)[1] == 0){
\begin{itemize}
\item FastQC: 0.11.10.devel
\item Trimmomatic: 0.39
\item BWA: 0.7.17-r1198-dirty
\item bwa-mem2: 2.2.1
\item bam-readcount: 0.8.0-unstable-7-625eea2
\item samtools 1.10
\item GATK: 3.8-1-0-gf15c1c3ef
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2 changes: 1 addition & 1 deletion RScripts/Report_Panel.Rnw
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Expand Up @@ -442,7 +442,7 @@ if(dim(som_all$muts_tab)[1] == 0) {
\begin{itemize}
\item FastQC: 0.11.10.devel
\item Trimmomatic: 0.39
\item BWA: 0.7.17-r1198-dirty
\item bwa-mem2: 2.2.1
\item bam-readcount: 0.8.0-unstable-7-625eea2
\item samtools 1.10
\item GATK: 3.8-1-0-gf15c1c3ef
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2 changes: 1 addition & 1 deletion RScripts/Report_tumorOnly.Rnw
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Expand Up @@ -413,7 +413,7 @@ if(dim(som_all$muts_tab)[1] == 0) {
\begin{itemize}
\item FastQC: 0.11.10.devel
\item Trimmomatic: 0.39
\item BWA: 0.7.17-r1198-dirty
\item bwa-mem2: 2.2.1
\item bam-readcount: 0.8.0-unstable-7-625eea2
\item samtools 1.10
\item GATK: 3.8-1-0-gf15c1c3ef
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4 changes: 4 additions & 0 deletions make_alignment.sh
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Expand Up @@ -130,6 +130,10 @@ ${BIN_FASTQC} "${fastq_o1_p_t}" -o "${DIR_WES}"
${BIN_FASTQC} "${fastq_o2_p_t}" -o "${DIR_WES}"

# make bam
if [ ! -f "${FILE_GENOME}.bwt.2bit.64" ]; then
echo "bwa-mem2 index not existing. Generating ..."
${BIN_BWAMEMINDEX} ${FILE_GENOME}
fi
${BIN_BWAMEM} -R "@RG\tID:${NameD}\tSM:${NameD}\tPL:illumina\tLB:lib1\tPU:unit1" -t "${CFG_COMMON_CPUCORES}" "${FILE_GENOME}" \
"${fastq_o1_p_t}" "${fastq_o2_p_t}" | ${BIN_SAMVIEW} -bS - >"${bam}"

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4 changes: 4 additions & 0 deletions make_panel_alignment.sh
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Expand Up @@ -135,6 +135,10 @@ do
${BIN_FASTQC} ${fastq_o2_p_t} -o ${DIR_WES}

# make bam
if [ ! -f "${FILE_GENOME}.bwt.2bit.64" ]; then
echo "bwa-mem2 index not existing. Generating ..."
${BIN_BWAMEMINDEX} ${FILE_GENOME}
fi
${BIN_BWAMEM} -R "@RG\tID:${NameD}\tSM:${NameD}\tPL:illumina\tLB:lib1\tPU:unit1" -t "${CFG_COMMON_CPUCORES}" "${FILE_GENOME}" \
${fastq_o1_p_t} ${fastq_o2_p_t} | ${BIN_SAMVIEW} -bS - > ${tmpbam}

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4 changes: 4 additions & 0 deletions make_tumorOnly_alignment.sh
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Expand Up @@ -127,6 +127,10 @@ ${BIN_FASTQC} "${fastq_o1_p_t}" -o "${DIR_WES}"
${BIN_FASTQC} "${fastq_o2_p_t}" -o "${DIR_WES}"

# make bam
if [ ! -f "${FILE_GENOME}.bwt.2bit.64" ]; then
echo "bwa-mem2 index not existing. Generating ..."
${BIN_BWAMEMINDEX} ${FILE_GENOME}
fi
${BIN_BWAMEM} -R "@RG\tID:${NameD}\tSM:${NameD}\tPL:illumina\tLB:lib1\tPU:unit1" -t "${CFG_COMMON_CPUCORES}" "${FILE_GENOME}" \
"${fastq_o1_p_t}" "${fastq_o2_p_t}" | ${BIN_SAMVIEW} -bS - >"${bam}"

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4 changes: 3 additions & 1 deletion programs.cfg.sh
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Expand Up @@ -292,7 +292,8 @@ readonly DIR_TRIMMOMATIC_ADAPTER="${DIR_TOOLS}/Trimmomatic/adapters"
readonly BIN_CUT="cut -f1,2,3"

# Alignment
readonly BIN_BWAMEM="${DIR_TOOLS}/bwa/bwa mem -M "
readonly BIN_BWAMEM="${DIR_TOOLS}/bwa-mem2/bwa-mem2 mem -M "
readonly BIN_BWAMEMINDEX="${DIR_TOOLS}/bwa-mem2/bwa-mem2 index"

# BAM-Readcount
readonly BIN_BAM_READCOUNT="${DIR_TOOLS}/bam-readcount/bin/bam-readcount -q ${CFG_SAMTOOLS_MPILEUP_MINMQ} -b ${CFG_GENERAL_MINBASEQUAL} -w 1 -f ${FILE_GENOME} "
Expand Down Expand Up @@ -573,6 +574,7 @@ export DIR_TRIMMOMATIC_ADAPTER
export BIN_CUT

export BIN_BWAMEM
export BIN_BWAMEMINDEX

export BIN_BAM_READCOUNT

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1 change: 0 additions & 1 deletion tools/bwa
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Submodule bwa deleted from 3072c8
10 changes: 6 additions & 4 deletions tools/install.sh
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Expand Up @@ -131,11 +131,13 @@ mv ${DIR_SCRIPT}/bam-readcount/build/bin ${DIR_SCRIPT}/bam-readcount/bin
rm -rf ${DIR_SCRIPT}/bam-readcount/build

#######
# bwa #
# bwa-mem2 #
#######
cd ${DIR_SCRIPT}/bwa && make && chmod +x bwa
rm -f *.o

cd ${DIR_SCRIPT}
wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2 -O bwa-mem2.tar.bz2
tar -xf bwa-mem2.tar.bz2
rm bwa-mem2*.tar.bz2
mv bwa-mem2* bwa-mem2

##########
# htslib #
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