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README.md

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@@ -3,7 +3,7 @@ Detect and visualize target mutations by scanning FastQ files directly
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* Ultra sensitive.
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* 50X+ faster than normal pipeline (i.e. BWA + Samtools + GATK/VarScan/Mutect).
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* Very easy to use and need nothing else. No alignment, no reference genome, no variant call, no...
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* Contains most actionable mutation points for cancer, like EGFR L858R, BRAF V600E...
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* Contains most actionable mutation points for cancer, like EGFR p.L858R, BRAF p.V600E...
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* Beautiful and informative HTML report with informative pileup visualization.
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* Multi-threading support.
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* Supports both single-end and pair-end data.
@@ -67,7 +67,7 @@ mutscan -1 <read1_file_name>
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# Mutation file
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* Mutation file, specified by `-m`, can be a `CSV file`, or a `VCF file`.
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* If no `-m` specified, MutScan will use the built-in default mutation file with about 55 cancer related mutation points.
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* If no `-m` specified, MutScan will use the built-in default mutation file with about 60 cancer related mutation points.
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* If a CSV is provided, no reference genome assembly needed.
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* If a VCF is provided, corresponding reference genome assembly should be provided (i.e. ucsc.hg19.fasta), and should not be zipped.
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