Mercurial > repos > ulfschaefer > phephenix
comparison filter_vcf.xml @ 12:e252b0b9dd99 draft
Uploaded
| author | ulfschaefer |
|---|---|
| date | Thu, 16 Jun 2016 10:44:40 -0400 |
| parents | 74f595df6e51 |
| children | 48c41c6ad84e |
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| 11:a3f15f50a4af | 12:e252b0b9dd99 |
|---|---|
| 51 <option value="mq0_ratio_option">MQ0 ratio</option> | 51 <option value="mq0_ratio_option">MQ0 ratio</option> |
| 52 <option value="qual_score_option">Quality score</option> | 52 <option value="qual_score_option">Quality score</option> |
| 53 <option value="mq0f_ratio_option">MQ0F ratio</option> | 53 <option value="mq0f_ratio_option">MQ0F ratio</option> |
| 54 </param> | 54 </param> |
| 55 <when value="gq_score_option"> | 55 <when value="gq_score_option"> |
| 56 <param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer"/> | 56 <param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer."/> |
| 57 </when> | 57 </when> |
| 58 <when value="dp4_ratio_option"> | 58 <when value="dp4_ratio_option"> |
| 59 <param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float"/> | 59 <param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float. Only samtools mpileup before version 1.3."/> |
| 60 </when> | 60 </when> |
| 61 <when value="ad_ratio_option"> | 61 <when value="ad_ratio_option"> |
| 62 <param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float"/> | 62 <param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float. GATK only and samtools from version 1.3."/> |
| 63 </when> | 63 </when> |
| 64 <when value="mq_score_option"> | 64 <when value="mq_score_option"> |
| 65 <param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer"/> | 65 <param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer."/> |
| 66 </when> | 66 </when> |
| 67 <when value="min_depth_option"> | 67 <when value="min_depth_option"> |
| 68 <param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer"/> | 68 <param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer."/> |
| 69 </when> | 69 </when> |
| 70 <when value="uncall_gt_option"> | 70 <when value="uncall_gt_option"> |
| 71 <param name="uncall_gt" type="text" value="" hidden="True"/> | 71 <param name="uncall_gt" type="text" value="" hidden="True"/> |
| 72 </when> | 72 </when> |
| 73 <when value="mq0_ratio_option"> | 73 <when value="mq0_ratio_option"> |
| 74 <param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float"/> | 74 <param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float. GATK only."/> |
| 75 </when> | 75 </when> |
| 76 <when value="qual_score_option"> | 76 <when value="qual_score_option"> |
| 77 <param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer"/> | 77 <param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer."/> |
| 78 </when> | 78 </when> |
| 79 <when value="mq0f_ratio_option"> | 79 <when value="mq0f_ratio_option"> |
| 80 <param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float"/> | 80 <param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float. Samtools only."/> |
| 81 </when> | 81 </when> |
| 82 </conditional> | 82 </conditional> |
| 83 </repeat> | 83 </repeat> |
| 84 <param name="onlygood" type="select" label="Write only good variants to output" help="Write only variants that PASS all filters. "> | 84 <param name="onlygood" type="select" label="Write only good variants to output" help="Write only variants that PASS all filters. "> |
| 85 <option value="true" selected="true">Write all</option> | 85 <option value="true" selected="true">Write all</option> |