Mercurial > repos > devteam > picard
annotate test-data/picard_CollectWgsMetrics_test1.tab @ 30:b502c227b5e6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
| author | iuc |
|---|---|
| date | Mon, 22 Aug 2022 09:56:00 +0000 |
| parents | 5053a18d9bc8 |
| children | 3f254c5ced1d |
| rev | line source |
|---|---|
| 5 | 1 ## htsjdk.samtools.metrics.StringHeader |
|
19
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
12
diff
changeset
|
2 # CollectWgsMetrics INPUT=picard_CollectWgsMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_43.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 USE_FAST_ALGORITHM=false READ_LENGTH=150 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false |
| 5 | 3 ## htsjdk.samtools.metrics.StringHeader |
|
19
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
12
diff
changeset
|
4 # Started on: Sat Apr 14 09:30:46 CEST 2018 |
| 5 | 5 |
| 6 ## METRICS CLASS picard.analysis.CollectWgsMetrics$WgsMetrics | |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
5
diff
changeset
|
7 GENOME_TERRITORY MEAN_COVERAGE SD_COVERAGE MEDIAN_COVERAGE MAD_COVERAGE PCT_EXC_MAPQ PCT_EXC_DUPE PCT_EXC_UNPAIRED PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_CAPPED PCT_EXC_TOTAL PCT_1X PCT_5X PCT_10X PCT_15X PCT_20X PCT_25X PCT_30X PCT_40X PCT_50X PCT_60X PCT_70X PCT_80X PCT_90X PCT_100X HET_SNP_SENSITIVITY HET_SNP_Q |
|
19
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
12
diff
changeset
|
8 16568 2.915862 3.835741 2 2 0 0 0 0.000041 0.008069 0 0.00811 0.684633 0.240464 0.055831 0.02541 0.010985 0 0 0 0 0 0 0 0 0 0.544024 3 |
| 5 | 9 |
| 10 ## HISTOGRAM java.lang.Integer | |
|
19
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
12
diff
changeset
|
11 coverage high_quality_coverage_count |
| 5 | 12 0 5225 |
| 13 1 3010 | |
| 14 2 1806 | |
| 15 3 1333 | |
| 16 4 1210 | |
| 17 5 1247 | |
| 18 6 672 | |
| 19 7 468 | |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
5
diff
changeset
|
20 8 362 |
|
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
5
diff
changeset
|
21 9 310 |
| 5 | 22 10 210 |
| 23 11 95 | |
| 24 12 78 | |
| 25 13 52 | |
| 26 14 69 | |
| 27 15 64 | |
| 28 16 29 | |
| 29 17 31 | |
| 30 18 53 | |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
5
diff
changeset
|
31 19 62 |
|
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
5
diff
changeset
|
32 20 64 |
| 5 | 33 21 74 |
| 34 22 32 | |
| 35 23 12 | |
| 36 24 0 | |
| 37 25 0 | |
| 38 26 0 | |
| 39 27 0 | |
| 40 28 0 | |
| 41 29 0 | |
| 42 30 0 | |
| 43 31 0 | |
| 44 32 0 | |
| 45 33 0 | |
| 46 34 0 | |
| 47 35 0 | |
| 48 36 0 | |
| 49 37 0 | |
| 50 38 0 | |
| 51 39 0 | |
| 52 40 0 | |
| 53 41 0 | |
| 54 42 0 | |
| 55 43 0 | |
| 56 44 0 | |
| 57 45 0 | |
| 58 46 0 | |
| 59 47 0 | |
| 60 48 0 | |
| 61 49 0 | |
| 62 50 0 | |
| 63 51 0 | |
| 64 52 0 | |
| 65 53 0 | |
| 66 54 0 | |
| 67 55 0 | |
| 68 56 0 | |
| 69 57 0 | |
| 70 58 0 | |
| 71 59 0 | |
| 72 60 0 | |
| 73 61 0 | |
| 74 62 0 | |
| 75 63 0 | |
| 76 64 0 | |
| 77 65 0 | |
| 78 66 0 | |
| 79 67 0 | |
| 80 68 0 | |
| 81 69 0 | |
| 82 70 0 | |
| 83 71 0 | |
| 84 72 0 | |
| 85 73 0 | |
| 86 74 0 | |
| 87 75 0 | |
| 88 76 0 | |
| 89 77 0 | |
| 90 78 0 | |
| 91 79 0 | |
| 92 80 0 | |
| 93 81 0 | |
| 94 82 0 | |
| 95 83 0 | |
| 96 84 0 | |
| 97 85 0 | |
| 98 86 0 | |
| 99 87 0 | |
| 100 88 0 | |
| 101 89 0 | |
| 102 90 0 | |
| 103 91 0 | |
| 104 92 0 | |
| 105 93 0 | |
| 106 94 0 | |
| 107 95 0 | |
| 108 96 0 | |
| 109 97 0 | |
| 110 98 0 | |
| 111 99 0 | |
| 112 100 0 | |
| 113 101 0 | |
| 114 102 0 | |
| 115 103 0 | |
| 116 104 0 | |
| 117 105 0 | |
| 118 106 0 | |
| 119 107 0 | |
| 120 108 0 | |
| 121 109 0 | |
| 122 110 0 | |
| 123 111 0 | |
| 124 112 0 | |
| 125 113 0 | |
| 126 114 0 | |
| 127 115 0 | |
| 128 116 0 | |
| 129 117 0 | |
| 130 118 0 | |
| 131 119 0 | |
| 132 120 0 | |
| 133 121 0 | |
| 134 122 0 | |
| 135 123 0 | |
| 136 124 0 | |
| 137 125 0 | |
| 138 126 0 | |
| 139 127 0 | |
| 140 128 0 | |
| 141 129 0 | |
| 142 130 0 | |
| 143 131 0 | |
| 144 132 0 | |
| 145 133 0 | |
| 146 134 0 | |
| 147 135 0 | |
| 148 136 0 | |
| 149 137 0 | |
| 150 138 0 | |
| 151 139 0 | |
| 152 140 0 | |
| 153 141 0 | |
| 154 142 0 | |
| 155 143 0 | |
| 156 144 0 | |
| 157 145 0 | |
| 158 146 0 | |
| 159 147 0 | |
| 160 148 0 | |
| 161 149 0 | |
| 162 150 0 | |
| 163 151 0 | |
| 164 152 0 | |
| 165 153 0 | |
| 166 154 0 | |
| 167 155 0 | |
| 168 156 0 | |
| 169 157 0 | |
| 170 158 0 | |
| 171 159 0 | |
| 172 160 0 | |
| 173 161 0 | |
| 174 162 0 | |
| 175 163 0 | |
| 176 164 0 | |
| 177 165 0 | |
| 178 166 0 | |
| 179 167 0 | |
| 180 168 0 | |
| 181 169 0 | |
| 182 170 0 | |
| 183 171 0 | |
| 184 172 0 | |
| 185 173 0 | |
| 186 174 0 | |
| 187 175 0 | |
| 188 176 0 | |
| 189 177 0 | |
| 190 178 0 | |
| 191 179 0 | |
| 192 180 0 | |
| 193 181 0 | |
| 194 182 0 | |
| 195 183 0 | |
| 196 184 0 | |
| 197 185 0 | |
| 198 186 0 | |
| 199 187 0 | |
| 200 188 0 | |
| 201 189 0 | |
| 202 190 0 | |
| 203 191 0 | |
| 204 192 0 | |
| 205 193 0 | |
| 206 194 0 | |
| 207 195 0 | |
| 208 196 0 | |
| 209 197 0 | |
| 210 198 0 | |
| 211 199 0 | |
| 212 200 0 | |
| 213 201 0 | |
| 214 202 0 | |
| 215 203 0 | |
| 216 204 0 | |
| 217 205 0 | |
| 218 206 0 | |
| 219 207 0 | |
| 220 208 0 | |
| 221 209 0 | |
| 222 210 0 | |
| 223 211 0 | |
| 224 212 0 | |
| 225 213 0 | |
| 226 214 0 | |
| 227 215 0 | |
| 228 216 0 | |
| 229 217 0 | |
| 230 218 0 | |
| 231 219 0 | |
| 232 220 0 | |
| 233 221 0 | |
| 234 222 0 | |
| 235 223 0 | |
| 236 224 0 | |
| 237 225 0 | |
| 238 226 0 | |
| 239 227 0 | |
| 240 228 0 | |
| 241 229 0 | |
| 242 230 0 | |
| 243 231 0 | |
| 244 232 0 | |
| 245 233 0 | |
| 246 234 0 | |
| 247 235 0 | |
| 248 236 0 | |
| 249 237 0 | |
| 250 238 0 | |
| 251 239 0 | |
| 252 240 0 | |
| 253 241 0 | |
| 254 242 0 | |
| 255 243 0 | |
| 256 244 0 | |
| 257 245 0 | |
| 258 246 0 | |
| 259 247 0 | |
| 260 248 0 | |
| 261 249 0 | |
| 262 250 0 | |
| 263 |