### samtools faidx reference/ref.fa


### bwa index reference/ref.fa

[bwa_index] Pack FASTA... 0.04 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 2.34 seconds elapse.
[bwa_index] Update BWT... 0.04 sec
[bwa_index] Pack forward-only FASTA... 0.03 sec
[bwa_index] Construct SA from BWT and Occ... 0.61 sec
[main] Version: 0.7.12-r1039
[main] CMD: bwa index reference/ref.fa
[main] Real time: 3.079 sec; CPU: 3.060 sec

### (bwa mem  -v 2 -M -R '@RG	ID:snps	SM:snps' -t 1 reference/ref.fa /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_1.fq /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_2.fq | samtools view -@ 1 -q 60 -F 3844 -S -b -u -T ref.fa - | samtools sort -@ 1 - snps)

[samfaipath] fail to read file ref.fa.
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (429, 488, 536)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (215, 750)
[M::mem_pestat] mean and std.dev: (479.53, 81.93)
[M::mem_pestat] low and high boundaries for proper pairs: (108, 857)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.12-r1039
[main] CMD: bwa mem -v 2 -M -R @RG	ID:snps	SM:snps -t 1 reference/ref.fa /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_1.fq /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_2.fq
[main] Real time: 0.268 sec; CPU: 0.262 sec

### samtools index snps.bam


### samtools depth -q 20 snps.bam | bgzip > snps.depth.gz


### tabix -s 1 -b 2 -e 2 snps.depth.gz


### fasta_generate_regions.py reference/ref.fa.fai 1397543 > reference/ref.txt


### freebayes-parallel reference/ref.txt 1 -p 1 -q 20 -m 60 -F 0.9 -C 10 -V -f reference/ref.fa snps.bam > snps.raw.vcf

WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1397543..2795086

### vcffilter -f 'DP > 9' -f 'QUAL > 10' snps.raw.vcf > snps.vcf


### bgzip -c snps.vcf > snps.vcf.gz


### tabix -p vcf snps.vcf.gz


### /usr/local/Cellar/snippy/2.6/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 0 SNPs to TAB format.

### vcf-consensus snps.vcf.gz < reference/ref.fa > snps.consensus.fa