### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data

### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir out --ref wildtype.fna --R1 mutant_R1.fastq --R2 mutant_R2.fastq

### samtools faidx reference/ref.fa


### bwa index reference/ref.fa

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.03 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.02 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index reference/ref.fa
[main] Real time: 0.060 sec; CPU: 0.053 sec

### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa


### ln -sf reference/ref.fa .


### ln -sf reference/ref.fa.fai .


### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz


### bwa mem  -Y -M -R '@RG\tID:out\tSM:out' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.19210. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.19210. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.19210. -r -s - - > snps.bam

READ 24871 WRITTEN 24858 
EXCLUDED 0 EXAMINED 24871
PAIRED 24782 SINGLE 89
DULPICATE PAIR 10 DUPLICATE SINGLE 3
DUPLICATE TOTAL 13

### samtools index snps.bam


### fasta_generate_regions.py reference/ref.fa.fai 13379 > reference/ref.txt


### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05  -f reference/ref.fa snps.bam > snps.raw.vcf


### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf


### cp snps.filt.vcf snps.vcf


### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab

Loading reference: reference/ref.fa
Loaded 1 sequences.
Loading features: reference/ref.gff
Parsing variants: snps.vcf
Converted 16 SNPs to TAB format.

### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf


### bcftools convert -Oz -o snps.vcf.gz snps.vcf


### bcftools index -f snps.vcf.gz


### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz

Note: the --sample option not given, applying all records regardless of the genotype

### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf


### bcftools index -f snps.subs.vcf.gz


### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz

Note: the --sample option not given, applying all records regardless of the genotype

### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi