... | @@ -4,7 +4,10 @@ When the column GENE dispays the name of the gene associated with "_t00n", there |
... | @@ -4,7 +4,10 @@ When the column GENE dispays the name of the gene associated with "_t00n", there |
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The word "gap" in ALT, EFFECT, IMPACT or AA columns indicates a spanning deletion (see https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-)
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The word "gap" in ALT, EFFECT, IMPACT or AA columns indicates a spanning deletion (see https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-)
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The QD column shows the QualByDepth score given by GATK software, i.e. the QUAL score normalized by allele depth (AD) for a variant. For further information, check this page : https://gatk.broadinstitute.org/hc/en-us/articles/360037592191-QualByDepth
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The QD column shows the QualByDepth score given by GATK software, i.e. the QUAL score normalized by allele depth (AD) for a variant. For further information, check this page : https://gatk.broadinstitute.org/hc/en-us/articles/360037592191-QualByDepth/
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For further information about how snpEff annotates effects and impacts, check this page :
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https://pcingola.github.io/SnpEff/se_inputoutput/
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A "md" in EFFECT, IMPACT or AA columns stands for "missing data".
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A "md" in EFFECT, IMPACT or AA columns stands for "missing data".
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