| ... | ... | @@ -6,9 +6,7 @@ Then variants were filtered again based on certain criteria. Were removed from f |
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- FS (FisherStrand) > 60.0
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- SOR (StrandOddsRatio) > 3.0
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- MQ (RMSMappingQuality) < 40.0
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For further information on criteria, take a look on the page below :
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https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants
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For further information on criteria, take a look at this page : https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants
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The phylogenic tree was generated using SNPhylo.20181005, with a bootstrap confidence value of 100, and Pathenocissus as outgroup.
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The online software iTOL was used to display and annotate the tree. |
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