### echo snippy 4.4.5
### cd /galaxy-repl/main/jobdir/027/128/27128218/working

### /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/snippy --outdir https___raw_githubusercontent_com_galaxyproject_tools_iuc_master_tools_snippy_test_data_mutant_R1_fastq --cpus 1 --ram 7 --ref ref.fna --mapqual 60 --mincov 10 --minfrac 0.9 --minqual 100.0 --R1 /galaxy-repl/main/files/037/616/dataset_37616341.dat --R2 /galaxy-repl/main/files/037/616/dataset_37616403.dat

### 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] 0.06 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... 0.03 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index reference/ref.fa
[main] Real time: 0.128 sec; CPU: 0.104 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:https___raw_githubusercontent_com_galaxyproject_tools_iuc_master_tools_snippy_test_data_mutant_R1_fastq\tSM:https___raw_githubusercontent_com_galaxyproject_tools_iuc_master_tools_snippy_test_data_mutant_R1_fastq' -t 1 reference/ref.fa /galaxy-repl/main/files/037/616/dataset_37616341.dat /galaxy-repl/main/files/037/616/dataset_37616403.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /galaxy-repl/main/jobdir/027/128/27128218/_job_tmp --threads 1 -m 3500M | samtools fixmate -m - - | samtools sort -l 0 -T /galaxy-repl/main/jobdir/027/128/27128218/_job_tmp --threads 1 -m 3500M | samtools markdup -T /galaxy-repl/main/jobdir/027/128/27128218/_job_tmp -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 200694 > reference/ref.txt


### freebayes-parallel reference/ref.txt 1 -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>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' 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


### /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/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 15 SNPs to TAB format.

### /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/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