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| export THREADS=40 | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR187/008/ERR1873558/ERR1873558_1.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR187/008/ERR1873558/ERR1873558_2.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR210/001/SRR2101051/SRR2101051_1.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR210/001/SRR2101051/SRR2101051_2.fastq.gz | |
| wget ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| gunzip Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| mv Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa H37Rv.fa | |
| git clone https://github.com/lh3/bwa.git && cd bwa && make && cd ../ | |
| wget https://github.com/samtools/bcftools/releases/download/1.8/bcftools-1.8.tar.bz2 && tar -xvf bcftools-1.8.tar.bz2 && cd bcftools-1.8 && make && cd ../ | |
| wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2 && tar -xvf samtools-1.8.tar.bz2 && cd samtools-1.8/ && make && cd ../ | |
| bwa index H37Rv.fa | |
| bwa mem -t $THREADS H37Rv.fa ERR1873558_1.fastq.gz ERR1873558_2.fastq.gz | ./samtools-1.8/samtools view -@ $THREADS -b | ./samtools-1.8/samtools sort -@ $THREADS -o ERR1873558.bam - | |
| bwa mem -t $THREADS H37Rv.fa SRR2101051_1.fastq.gz SRR2101051_2.fastq.gz | ./samtools-1.8/samtools view -@ $THREADS -b | ./samtools-1.8/samtools sort -@ $THREADS -o SRR2101051.bam - | |
| ./bcftools-1.8/bcftools mpileup -f H37Rv.fa ERR1873558.bam -a DP | ./bcftools-1.8/bcftools call -mg 10 | bcftools convert --gvcf2vcf --f-ref H37Rv.fa | bcftools view -H | head | |
| ./bcftools-1.8/bcftools mpileup -f H37Rv.fa ERR1873558.bam -a DP | ./bcftools-1.8/bcftools call -mg 10 | bcftools convert --gvcf2vcf --f-ref H37Rv.fa -O u | bcftools view -H | head | |
| ./bcftools-1.8/bcftools mpileup -f H37Rv.fa ERR1873558.bam -a DP | ./bcftools-1.8/bcftools call -mg 10 -V indels -Ob -o ERR1873558.bcf | |
| ./bcftools-1.8/bcftools mpileup -f H37Rv.fa SRR2101051.bam -a DP | ./bcftools-1.8/bcftools call -mg 10 -V indels -Ob -o SRR2101051.bcf | |
| bcftools index ERR1873558.bcf | |
| bcftools index SRR2101051.bcf | |
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