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Update README.md
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jiyunmaths authored Aug 25, 2021
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Expand Up @@ -50,7 +50,7 @@ Options:
-n INT number of cores specified (default=1)
Example:
MuSE call f Reference.Genome O Output.Prefix -n 20 Tumor.bam Matched.Normal.bam
MuSE call -f Reference.Genome -O Output.Prefix -n 20 Tumor.bam Matched.Normal.bam
```

The second step, `MuSE sump`, takes as input the output file from `MuSE call` and File (3). This step computes tier-based cutoffs from a sample-specific error model. We provide two options for building the model, one for WES data (option `-E`), and the other for WGS data (option `-G`).
Expand All @@ -67,7 +67,7 @@ Options:
genome used in 'MuSE call'
Example:
MuSE sump -I Output.Prefix.MuSE.txt -G O Output.Prefix.vcf D dbsnp.vcf.gz
MuSE sump -I Output.Prefix.MuSE.txt -G -O Output.Prefix.vcf -D dbsnp.vcf.gz
```

## Output of MuSE
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