Mercurial > repos > dfornika > snippy
annotate test-data/b_out_dev/snps.log @ 21:0e733df972b5 draft
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
author | dfornika |
---|---|
date | Tue, 12 Mar 2019 17:37:29 -0400 |
parents | |
children |
rev | line source |
---|---|
21
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
1 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
2 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
3 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir b_out_dev --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
4 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
5 ### samtools faidx reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
6 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
7 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
8 ### bwa index reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
9 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
10 [bwa_index] Pack FASTA... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
11 [bwa_index] Construct BWT for the packed sequence... |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
12 [bwa_index] 0.00 seconds elapse. |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
13 [bwa_index] Update BWT... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
14 [bwa_index] Pack forward-only FASTA... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
15 [bwa_index] Construct SA from BWT and Occ... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
16 [main] Version: 0.7.17-r1188 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
17 [main] CMD: bwa index reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
18 [main] Real time: 0.009 sec; CPU: 0.003 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
19 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
20 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
21 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
22 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
23 ### ln -sf reference/ref.fa . |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
24 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
25 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
26 ### ln -sf reference/ref.fa.fai . |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
27 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
28 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
29 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
30 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
31 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
32 ### bwa mem -Y -M -R '@RG\tID:b_out_dev\tSM:b_out_dev' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.9396. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.9396. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.9396. -r -s - - > snps.bam |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
33 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
34 READ 10 WRITTEN 10 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
35 EXCLUDED 0 EXAMINED 10 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
36 PAIRED 10 SINGLE 0 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
37 DULPICATE PAIR 0 DUPLICATE SINGLE 0 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
38 DUPLICATE TOTAL 0 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
39 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
40 ### samtools index snps.bam |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
41 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
42 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
43 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
44 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
45 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
46 ### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
47 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
48 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
49 ### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (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 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
50 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
51 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
52 ### cp snps.filt.vcf snps.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
53 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
54 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
55 ### /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 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
56 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
57 Loading reference: reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
58 Loaded 1 sequences. |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
59 Loading features: reference/ref.gff |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
60 Parsing variants: snps.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
61 Converted 1 SNPs to TAB format. |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
62 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
63 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
64 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
65 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
66 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
67 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
68 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
69 ### bcftools index -f snps.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
70 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
71 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
72 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
73 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
74 Note: the --sample option not given, applying all records regardless of the genotype |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
75 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
76 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
77 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
78 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
79 ### bcftools index -f snps.subs.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
80 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
81 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
82 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
83 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
84 Note: the --sample option not given, applying all records regardless of the genotype |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
85 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
86 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
87 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
88 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
89 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
90 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --force --outdir b_out_dev --rgid b --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
91 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
92 ### samtools faidx reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
93 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
94 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
95 ### bwa index reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
96 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
97 [bwa_index] Pack FASTA... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
98 [bwa_index] Construct BWT for the packed sequence... |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
99 [bwa_index] 0.00 seconds elapse. |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
100 [bwa_index] Update BWT... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
101 [bwa_index] Pack forward-only FASTA... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
102 [bwa_index] Construct SA from BWT and Occ... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
103 [main] Version: 0.7.17-r1188 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
104 [main] CMD: bwa index reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
105 [main] Real time: 0.008 sec; CPU: 0.002 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
106 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
107 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
108 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
109 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
110 ### ln -sf reference/ref.fa . |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
111 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
112 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
113 ### ln -sf reference/ref.fa.fai . |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
114 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
115 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
116 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
117 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
118 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
119 ### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.10001. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.10001. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.10001. -r -s - - > snps.bam |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
120 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
121 READ 10 WRITTEN 10 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
122 EXCLUDED 0 EXAMINED 10 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
123 PAIRED 10 SINGLE 0 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
124 DULPICATE PAIR 0 DUPLICATE SINGLE 0 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
125 DUPLICATE TOTAL 0 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
126 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
127 ### samtools index snps.bam |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
128 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
129 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
130 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
131 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
132 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
133 ### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
134 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
135 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
136 ### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (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 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
137 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
138 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
139 ### cp snps.filt.vcf snps.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
140 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
141 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
142 ### /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 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
143 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
144 Loading reference: reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
145 Loaded 1 sequences. |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
146 Loading features: reference/ref.gff |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
147 Parsing variants: snps.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
148 Converted 1 SNPs to TAB format. |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
149 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
150 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
151 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
152 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
153 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
154 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
155 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
156 ### bcftools index -f snps.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
157 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
158 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
159 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
160 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
161 Note: the --sample option not given, applying all records regardless of the genotype |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
162 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
163 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
164 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
165 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
166 ### bcftools index -f snps.subs.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
167 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
168 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
169 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
170 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
171 Note: the --sample option not given, applying all records regardless of the genotype |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
172 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
173 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
174 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
175 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
176 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
177 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --force --outdir b_out_dev --rgid b --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
178 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
179 ### samtools faidx reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
180 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
181 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
182 ### bwa index reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
183 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
184 [bwa_index] Pack FASTA... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
185 [bwa_index] Construct BWT for the packed sequence... |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
186 [bwa_index] 0.00 seconds elapse. |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
187 [bwa_index] Update BWT... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
188 [bwa_index] Pack forward-only FASTA... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
189 [bwa_index] Construct SA from BWT and Occ... 0.00 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
190 [main] Version: 0.7.17-r1188 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
191 [main] CMD: bwa index reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
192 [main] Real time: 0.009 sec; CPU: 0.003 sec |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
193 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
194 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
195 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
196 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
197 ### ln -sf reference/ref.fa . |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
198 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
199 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
200 ### ln -sf reference/ref.fa.fai . |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
201 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
202 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
203 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
204 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
205 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
206 ### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.22109. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.22109. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.22109. -r -s - - > snps.bam |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
207 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
208 READ 10 WRITTEN 10 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
209 EXCLUDED 0 EXAMINED 10 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
210 PAIRED 10 SINGLE 0 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
211 DULPICATE PAIR 0 DUPLICATE SINGLE 0 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
212 DUPLICATE TOTAL 0 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
213 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
214 ### samtools index snps.bam |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
215 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
216 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
217 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
218 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
219 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
220 ### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
221 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
222 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
223 ### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (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 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
224 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
225 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
226 ### cp snps.filt.vcf snps.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
227 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
228 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
229 ### /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 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
230 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
231 Loading reference: reference/ref.fa |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
232 Loaded 1 sequences. |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
233 Loading features: reference/ref.gff |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
234 Parsing variants: snps.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
235 Converted 1 SNPs to TAB format. |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
236 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
237 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
238 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
239 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
240 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
241 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
242 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
243 ### bcftools index -f snps.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
244 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
245 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
246 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
247 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
248 Note: the --sample option not given, applying all records regardless of the genotype |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
249 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
250 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
251 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
252 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
253 ### bcftools index -f snps.subs.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
254 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
255 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
256 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
257 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
258 Note: the --sample option not given, applying all records regardless of the genotype |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
259 |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
260 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi |
0e733df972b5
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents:
diff
changeset
|
261 |