Mercurial > repos > jjohnson > pileup_to_vcf

annotate README @ 9:c0a6e8f595ec default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add option to set VCF ID field value, this can be used to ID germline variants for SnpSift
author Jim Johnson <jj@umn.edu>
date Thu, 11 Apr 2013 10:28:10 -0500
parents 07cd87e94fbe
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
07cd87e94fbe Add REAMDE
Jim Johnson <jj@umn.edu>
parents:
diff changeset
1 Cconverts the tabular pileup output from samtools mpileup to a VCF file.
07cd87e94fbe Add REAMDE
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 Filters on read coverage, base quality and the frequency of a variant.
07cd87e94fbe Add REAMDE
Jim Johnson <jj@umn.edu>
parents:
diff changeset
3 The VCF info is populated with a SAF tag that give the specific frequency (0 - 1) of a variant being observed.
07cd87e94fbe Add REAMDE
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 This is used for filtering in the mmuff ( Missense Mutation and Frameshift Finder) workflow.
9
c0a6e8f595ec Add option to set VCF ID field value, this can be used to ID germline variants for SnpSift
Jim Johnson <jj@umn.edu>
parents: 8
diff changeset
5 The VCF ID field can be optionally set, which can be used with SnpSift annotate or SnpSift filter.