bcftools query

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/009/SRR2099969/SRR2099969_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/009/SRR2099969/SRR2099969_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

# 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/dellytools/delly/releases/download/v0.8.1/delly_v0.8.1_linux_x86_64bit  && chmod 755 delly_v0.8.1_linux_x86_64bit

# Mapping and variant calling
./bwa/bwa index H37Rv.fa
./bwa/bwa mem -t 20  H37Rv.fa SRR2099969_1.fastq.gz SRR2099969_2.fastq.gz | ./samtools-1.9/samtools view -@ 20 -b - | ./samtools-1.9/samtools sort -@ 20 -o SRR2099969.bam - 
./samtools-1.9/samtools index SRR2099969.bam 
./delly_v0.8.1_linux_x86_64bit call -g H37Rv.fa -t DEL -o SRR2099969.bcf SRR2099969.bam
./bcftools-1.9/bcftools view -i '(RV/(RR+RV))>0.7 || (DV/(DR+DV))>0.7 ' SRR2099969.bcf   | ./bcftools-1.9/bcftools view -i '(END-POS)<50000' > SRR2099969.filt.vcf 

# Extracting from VCF
./bcftools-1.9/bcftools query -f '%POS\t%END\n' SRR2099969.filt.vcf 

# Extracting from BCF
./bcftools-1.9/bcftools view SRR2099969.filt.vcf -Ob -o SRR2099969.filt.bcf
./bcftools-1.9/bcftools query -f '%POS\t%END\n' SRR2099969.filt.bcf