Workflow
The mtDNA Variant Processor App supports both mtDNA D-Loop, custom regions, and whole genome samples. See Analysis Methods.
Nextera Adapter Trimming
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Nextera adapters are removed from the forward and reverse reads. |
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Trimming is repeated until there are no more than 3 adapter bases on the end of the read. |
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Reads are discarded when they are excessively trimmed or have short amplicons. |
Alignment
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BWA-MEM performs the alignment. |
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Circular alignment is handled across the origin by identifying the true start and end of reads. |
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Realigns regions with indels to improve alignment and shifts indels to a 3' alignment. |
Account for Primers
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Manifest identifies the primers and amplicons. |
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Removes primer contributions from the reads for accurate variant calling. |
Variant Calling
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Identifies nucleotides that are greater than the interpretation threshold for the position. |
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Generates percentage of reads for a nucleotide that exceeds the analysis threshold (at). |
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Generates a percentage of reads for a nucleotide that exceeds the interpretation threshold (it). |
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Generates the interpretation threshold indicator for positions that have a nucleotide between the analysis threshold and the interpretation threshold. |
Filtering and Scoring
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Removes reads that do not meet the minimum quality score for a base call. |
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Calculates a score from the minimum quality score for base call, alignment score, and presence of low abundance reads at the position. |
Output Files
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VCF files and BAM files. |
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Use the mtDNA Variant Analyzer App to view the analysis results. |
mtDNA Variant Processor v1.0 Online Help