Changes between Version 5 and Version 6 of SOPs/callingSNPs

Timestamp:

08/07/13 13:03:35 (11 years ago)

Author:

thiruvil

Comment:

--

SOPs/callingSNPs

@@ -49 +49 @@
 {{{
  #Use appropriate i) organism  and ii) annotation (eg. UCSC, RefSeq, Ensembl)
-  #Mouse: mm37 (UCSC/RefSeq), mm37.61 (Ensembl)
-  #Human: hg37 (UCSC/RefSeq), hg37.61 (Ensembl)
-  #Output is created in several files: an html summary file and text files with detailed information 
-  snpEff -vcf4 mm37.61 accepted_hits.raw.filtered.vcf > accepted_hits.raw.filtered.snpEff
+ #Mouse: mm37 (UCSC/RefSeq), mm37.61 (Ensembl)
+ #Human: hg37 (UCSC/RefSeq), hg37.61 (Ensembl)
+ #Output is created in several files: an html summary file and text files with detailed information 
+ #NOTE: snpEff requires a config file, .snpEff.config; annotating variants on the mitochondria (which has a different codon usage) needs to be specified in the config file, eg.
+ #GRCh37.71.genome : Homo_sapiens
+ #GRCh37.71.reference : ftp://ftp.ensembl.org/pub/release-71/gtf/
+ #GRCh37.71.MT.codonTable = Vertebrate_Mitochondrial (non-standard!)
+
+  snpEff GRCh37.71 variants.vcf > variants.annotated.vcf
 
 }}}