Galaxy | Published Workflow | Du Novo GTN tutorial - Variant calling

Du Novo GTN tutorial - Variant calling

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

Step	Annotation
Step 1: Input dataset Trimmed reads (mate 1) select at runtime
Step 2: Input dataset Trimmed reads (mate 2) select at runtime
Step 3: Map with BWA-MEM Will you select a reference genome from your history or use a built-in index? Use a built-in genome index Using reference genome hg38 Single or Paired-end reads Paired Select first set of reads Output dataset 'output' from step 1 Select second set of reads Output dataset 'output' from step 2 Enter mean, standard deviation, max, and min for insert lengths. Empty. Set read groups information? Do not set Select analysis mode 1.Simple Illumina mode Job Resource Parameters Use default job resource parameters
Step 4: BamLeftAlign Choose the source for the reference genome Locally cached Select alignment file in BAM format Output dataset 'bam_output' from step 3 Using reference genome hg38 Maximum number of iterations 5
Step 5: Naive Variant Caller (NVC) Choose the source for the reference list Locally cached BAM files BAM file 1 BAM file Output dataset 'output_bam' from step 4 Using reference genome hg38 Restrict to regions Restrict to regions 1 Chromosome chr9 Start Not available. End Not available. Restrict to regions by files Minimum number of reads needed to consider a REF/ALT 0 Minimum base quality 0 Minimum mapping quality 20 Ploidy 1 Only write out positions with possible alternate alleles False Report counts by strand True Show Advanced Options Hide Advanced Options
Step 6: Variant Annotator Input variants from Naive Variants Detector Output dataset 'output_vcf' from step 5 Minor allele frequency threshold 0.0 Coverage threshold 10 Do not filter sites or alleles False Output stranded base counts True Write header line True PRNG seed Empty.
Step 7: Filter Filter Output dataset 'output' from step 6 With following condition c16 >= 0.01 Number of header lines to skip 1

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nstoler

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