M. tuberculosis Map and Variant Call


StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: SnpEff download:
Mycobacterium_tuberculosis_h37rv
Step 5: Trimmomatic
Paired-end (two separate input files)
Output dataset 'output' from step 1
Output dataset 'output' from step 2
True
Standard
Nextera (paired-ended)
2
30
10
8
True
Trimmomatic Operations
Trimmomatic Operation 1
Sliding window trimming (SLIDINGWINDOW)
4
20
False
False
Step 6: Map with BWA-MEM
Use a genome from history and build index
Output dataset 'output' from step 3
Auto. Let BWA decide the best algorithm to use
Paired
Output dataset 'fastq_out_r1_paired' from step 5
Output dataset 'fastq_out_r2_paired' from step 5
Empty.
Set read groups (SAM/BAM specification)
True
True
ILLUMINA
False
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Not available.
Empty.
1.Simple Illumina mode
Use default job resource parameters
Step 7: MPileup
Use a genome from the history
Output dataset 'bam_output' from step 6
Output dataset 'output' from step 3
Perform genotype likelihood computation (--VCF, --BCF options)
VCF
False
Nothing selected.
Perform INDEL calling and set advanced options
40
20
100
250
1
0.002
False
Platform for INDEL candidates
Advanced
Do not filter
Do not limit
Do not exclude
False
False
False
50
250
False
30
13
Empty.
Step 8: bcftools call
Output dataset 'output_mpileup' from step 7
Restrict to:
None
Empty.
False
select at runtime
False
Consensus/variant calling Options:
Multiallelic and rare-variant Caller
Do not constrain
None
Empty.
Not available.
0.5
0.0011
File format Options:
1 - Treat all samples as haploid
select at runtime
None
Empty.
False
select at runtime
False
Input/output Options:
False
Empty.
False
Nothing selected.
False
uncompressed VCF
Step 9: SnpSift Filter
Output dataset 'output_file' from step 8
(QUAL > 30) & (DP > 5)
False
Retain entries that pass filter, remove other entries
Step 10: Text transformation
Output dataset 'output' from step 9
/^[^#]/s/^AL123456.3/Chromosome/
Hide Advanced Options
Step 11: SnpEff eff:
Output dataset 'output' from step 10
VCF
VCF (only if input is VCF)
Downloaded snpEff database in your history
Output dataset 'snpeff_db' from step 4
Regulation options:
None
5000 bases
2 bases
Use Defaults
Use 'EFF' field compatible with older versions (instead of 'ANN') Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C) Use one letter Amino acid codes in HGVS notation. E.g. p.R47G instead of p.Arg47Gly Use transcript ID in HGVS notation. E.g. ENST00000252100:c.914C>G instead of c.914C>G Only use canonical transcripts Only use protein coding transcripts Use gene ID instead of gene name (VCF output) Disable IUB code expansion in input variants Add OICR tag in VCF file Add loss of function (LOF) and nonsense mediated decay (NMD) tags
select at runtime
select at runtime
Nothing selected.
No
Use default (based on input type)
Empty.
True
True