Somatic Genotyping VCF
The Somatic Genotyping module generates a modified VCF file with records having a SOMATICSCORE key in the INFO field and a modified READSOURCES.
Values for READSOURCES (0:17:24,1:1:22) can be interpreted as follows:
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}
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17—Number of anomalous reads in tumor sample |
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}
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24—Normal reads in tumor sample |
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}
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1—Number of anomalous reads in normal sample |
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}
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22—Number of normal reads in normal sample |
Mantra tags some somatic structural variants as having low-confidence. The following VCF filter flags are used to indicate low-confidence:
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}
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MaxSVLEN—Somatic variants is larger than default length of 10Kb of confident SV calls. |
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}
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LowSomaticScore—Somatic variants with a Q-score of less than 30 are still listed in the output file. They are marked using this flag to indicate that they are of lower confidence. |
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}
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LowMAPQ—The fraction of reads that are non-anomalous and above the minimum MAPQ threshold in the normal sample is less than 0.8. |
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}
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MaxDepth—Normal sample site depth is greater than 3x the mean chromosome depth. |
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}
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NormalSupport—At least one read in the normal sample strongly supports the putative somatic allele. |
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}
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MinSampleCount—Fewer than 8 reads support any allele in one of the samples.
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