Changes between Version 30 and Version 31 of SOPs/variant_calling

Timestamp:

03/21/19 14:56:10 (6 years ago)

Author:

thiruvil

Comment:

--

SOPs/variant_calling

@@ -109 +109 @@
 == Annotate effect(s) of variants on genes ==
 
+  * snpEff
+
 Use snpEff (assuming snpEff has gene+protein annotations for your genome):
 {{{
@@ -118 +120 @@
 snpEff -c /usr/local/share/snpEff/snpEff.config -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -s A_snpEff.html SacCer_Apr2011.18 A_reads.bt2.sorted_unique.filtered.vcf > A_reads.bt2.sorted_unique.filtered.snpEff.vcf
 }}}
+
+
+  * Ensembl's Variant Effect Predictor (VEP)
+For large number of variants, download the annotation and use --cache or --offline instead of --database, see[[http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html | documentation]]
+{{{
+#default human, set by --species
+vep -i chr1_subset.vcf --database
+}}}
+
 
 See [wiki:SOPs/vcf Interpreting VCF files ] for more information.