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jodyphelan/setGT_bug.sh

Created October 16, 2019 20:18
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setGT_bug.sh
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR040/ERR040131/ERR040131_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR040/ERR040131/ERR040131_2.fastq.gz
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/195/955/GCF_000195955.2_ASM19595v2/GCF_000195955.2_ASM19595v2_genomic.fna.gz
gunzip GCF_000195955.2_ASM19595v2_genomic.fna.gz
mv GCF_000195955.2_ASM19595v2_genomic.fna H37Rv.fa
# Get software
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && tar -xvf samtools-1.9.tar.bz2 && cd samtools-1.9/ && make && cd ..
wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 && tar -xvf bcftools-1.9.tar.bz2 && cd bcftools-1.9/ && make && cd ..
git clone https://github.com/lh3/bwa.git && cd bwa && make && cd ../
wget https://github.com/broadinstitute/gatk/releases/download/4.1.4.0/gatk-4.1.4.0.zip
unzip gatk-4.1.4.0.zip
# Mapping and variant calling
./bwa/bwa index H37Rv.fa
./bwa/bwa mem -t 20 H37Rv.fa ERR040131_1.fastq.gz ERR040131_2.fastq.gz | ./samtools-1.9/samtools view -@ 20 -b - | ./samtools-1.9/samtools sort -@ 20 -o ERR040131.bam -
./samtools-1.9/samtools index ERR040131.bam
./bcftools-1.9/bcftools mpileup -f H37Rv.fa -r NC_000962.3:2638364-2640364 ERR040131.bam -a DP,AD | ./bcftools-1.9/bcftools call -mv -Oz -o ERR040131.vcf.gz
export BCFTOOLS_PLUGINS=$PWD/bcftools-1.9/plugins
./bcftools-1.9/bcftools +setGT ERR040131.vcf.gz -- -i 'GT="het"' -t q -n M
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