Mercurial > repos > jjohnson > snpeff_cds_report

annotate README @ 7:fbb6510186df default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
when codon has ambiguous nucleotide translate to X
author Jim Johnson <jj@umn.edu>
date Mon, 15 Sep 2014 06:13:47 -0500
parents cdbdac66d6b5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cdbdac66d6b5 Uploaded
jjohnson
parents:
diff changeset
1 snpeff_cds_report reports the protein coding changes that result from frame shift and non_synonymous variants.
cdbdac66d6b5 Uploaded
jjohnson
parents:
diff changeset
2 It requires the input to be from the MMuFF (Missense Mutation and Frameshift Finder) workflow.
cdbdac66d6b5 Uploaded
jjohnson
parents:
diff changeset
3 Specifically it requires the input from snpEff ( http://snpeff.sourceforge.net/ ) set with an Ensembl genome build,
cdbdac66d6b5 Uploaded
jjohnson
parents:
diff changeset
4 which will annotate variants with Ensembl transctipt IDs.