From 076ec2ac8a7b1488476454c36b6a23255bed1529 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 11 Feb 2020 12:11:37 +0000 Subject: [PATCH] JAL-3376 documentation for standard attributes for variants from VCF --- help/help/help.jhm | 1 + help/help/helpTOC.xml | 2 +- help/help/html/features/importvcf.html | 23 +++++++++++++++++++++++ 3 files changed, 25 insertions(+), 1 deletion(-) diff --git a/help/help/help.jhm b/help/help/help.jhm index 47f7d53..6b0a1c0 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -167,4 +167,5 @@ + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index 7e358d6..5374e1a 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -24,7 +24,7 @@ - + diff --git a/help/help/html/features/importvcf.html b/help/help/html/features/importvcf.html index e013472..511ff2e 100755 --- a/help/help/html/features/importvcf.html +++ b/help/help/html/features/importvcf.html @@ -49,6 +49,29 @@ retrieved from Ensembl.

+ Standard Variant Attributes +

+

Jalview decorates variant features imported from VCF files with + attributes that can be used to filter or shade variant annotation + including the following: +

+
    +
  • POS - Chromosomal position as recorded in VCF
  • +
  • ID - in GNOMAD releases specifies rs identifier of + a known dbSNP variant.
  • +
  • QUAL is the 'phred-scaled quality score' for the ALT + assertion (or quality of SNP call if there are no alternate + alleles). Higher is more confident.
  • +
  • FILTER is 'PASS' if all filters have been passed, + else a list of failed filters for the variant (e.g. poor quality, + or insufficient sample size).
  • +
+

Standard attributes were introduced in Jalview 2.11.1.0. VCF field semantics are highly dependent on the source of your VCF + file. See https://www.internationalgenome.org/wiki/Analysis/vcf4.0 + for more information. +

+

Working with variants from organisms other than H.sapiens.

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