Mercurial > repos > ulfschaefer > phephenix
changeset 15:48c41c6ad84e draft
Uploaded
author | ulfschaefer |
---|---|
date | Mon, 11 Jul 2016 10:50:16 -0400 |
parents | 2e5a83c0f78f |
children | 55bfe9d1888e |
files | filter_vcf.xml |
diffstat | 1 files changed, 19 insertions(+), 0 deletions(-) [+] |
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--- a/filter_vcf.xml Fri Jul 01 06:09:01 2016 -0400 +++ b/filter_vcf.xml Mon Jul 11 10:50:16 2016 -0400 @@ -115,5 +115,24 @@ \-\-only-good Write only variants that PASS all filters (default all variants are written). +----- + +Which filter can be used for your data depends on the variant caller that was used to create the VCF file. + +============= =============================================== +Filter Remark +============= =============================================== +GQ score Always available* +DP4 ratio Samtools mpileup before version 1.3 only* +AD ratio GATK and samtools mpileup from version 1.3 only +MQ score Always available* +Minimum depth Always available* +MQ0 ratio GATK only +Quality score Always available* +MQ0F ratio Samtools mpileup only* +============= =============================================== + +Filters marked with * are availabe for the workflow included with PHE Phenix. + </help> </tool>