X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fimportvcf.html;h=7b699eb3462c3d104eaf623410f76caa1f0805d7;hb=cfcd397b19f70fb39d6d21437db8eb6ffcac3914;hp=bbc9f78a872a6b508763b8bb16f52325e2d7dd60;hpb=7bb2a1c049e7b7be9c04012ce90afc173b81eb1a;p=jalview.git diff --git a/help/help/html/features/importvcf.html b/help/help/html/features/importvcf.html index bbc9f78..7b699eb 100755 --- a/help/help/html/features/importvcf.html +++ b/help/help/html/features/importvcf.html @@ -49,6 +49,47 @@ 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: +
+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 without CSQ fields +
++ Jalview 2.11.1's new virtual + features mean that peptide sequences are no longer annotated + directly with protein missense variants. This makes it harder to + filter variants when they do not already include the CSQ field. You + can rescue the pre-2.11.1 functionality by: +
+Working with variants from organisms other than H.sapiens.
@@ -57,7 +98,7 @@ ##reference header that define what species and assembly name the VCF was generated against.VCF_SPECIES=1000genomes=homo_sapiens,c_elegans=celegans