Mercurial > repos > ulfschaefer > phephenix

comparison filter_vcf.xml @ 15:48c41c6ad84e draft

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author ulfschaefer
date Mon, 11 Jul 2016 10:50:16 -0400
parents e252b0b9dd99
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14:2e5a83c0f78f 15:48c41c6ad84e
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114 \-\-reference REFERENCE, -r REFERENCE mpileup versions 1.3 and before do not output all positions. This is required to fix reference base in VCF. 114 \-\-reference REFERENCE, -r REFERENCE mpileup versions 1.3 and before do not output all positions. This is required to fix reference base in VCF.
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116 \-\-only-good Write only variants that PASS all filters (default all variants are written). 116 \-\-only-good Write only variants that PASS all filters (default all variants are written).
117 117
118 -----
119
120 Which filter can be used for your data depends on the variant caller that was used to create the VCF file.
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122 ============= ===============================================
123 Filter Remark
124 ============= ===============================================
125 GQ score Always available*
126 DP4 ratio Samtools mpileup before version 1.3 only*
127 AD ratio GATK and samtools mpileup from version 1.3 only
128 MQ score Always available*
129 Minimum depth Always available*
130 MQ0 ratio GATK only
131 Quality score Always available*
132 MQ0F ratio Samtools mpileup only*
133 ============= ===============================================
134
135 Filters marked with * are availabe for the workflow included with PHE Phenix.
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118 </help> 137 </help>
119 </tool> 138 </tool>