Du Novo GTN tutorial - Variant calling

Annotation: Run this on the trimmed consensus reads (DCS or SSCS) from Du Novo.

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Map with BWA-MEM
Use a built-in genome index
hg38
Paired
Output dataset 'output' from step 1
Output dataset 'output' from step 2
Empty.
Do not set
1.Simple Illumina mode
Use default job resource parameters
Step 4: BamLeftAlign
Locally cached
Output dataset 'bam_output' from step 3
hg38
5
Step 5: Naive Variant Caller (NVC)
Locally cached
BAM files
BAM file 1
Output dataset 'output_bam' from step 4
hg38
Restrict to regions
Restrict to regions 1
chr9
Not available.
Not available.
Restrict to regions by files
0
0
20
1
False
True
Hide Advanced Options
Step 6: Variant Annotator
Output dataset 'output_vcf' from step 5
0.0
10
False
True
True
Empty.
Step 7: Filter
Output dataset 'output' from step 6
c16 >= 0.01
1