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Commit message:
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modified:
filter_vcf.xml |
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| diff -r 2e5a83c0f78f -r 48c41c6ad84e filter_vcf.xml --- a/filter_vcf.xml Fri Jul 01 06:09:01 2016 -0400 +++ b/filter_vcf.xml Mon Jul 11 10:50:16 2016 -0400 |
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| @@ -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> |