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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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