Mercurial > repos > devteam > picard
annotate test-data/pos_summary @ 24:b9fbec5ac6b2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
| author | iuc |
|---|---|
| date | Fri, 31 May 2019 03:21:52 -0400 |
| parents | 1cd1cf786389 |
| children | 3f254c5ced1d |
| rev | line source |
|---|---|
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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1 ## htsjdk.samtools.metrics.StringHeader |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
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changeset
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2 # CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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3 ## htsjdk.samtools.metrics.StringHeader |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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4 # Started on: Fri May 03 21:58:49 EDT 2019 |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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5 |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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6 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasSummaryMetrics |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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7 SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE TOTAL_QSCORE WORST_CXT WORST_CXT_QSCORE WORST_PRE_CXT WORST_PRE_CXT_QSCORE WORST_POST_CXT WORST_POST_CXT_QSCORE ARTIFACT_NAME |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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8 sample-a tumor-a A C 35 TAA 26 CAN 34 NAA 28 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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9 sample-a tumor-a A G 16 TAT 9 TAN 11 NAT 12 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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10 sample-a tumor-a A T 100 AAA 100 AAN 100 NAA 100 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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11 sample-a tumor-a C A 100 ACA 100 ACN 100 NCA 100 Cref |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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12 sample-a tumor-a C G 100 ACA 100 ACN 100 NCA 100 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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13 sample-a tumor-a C T 100 TCA 29 ACN 100 NCA 34 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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14 sample-a tumor-a G A 34 CGA 23 AGN 28 NGA 30 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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15 sample-a tumor-a G C 36 TGC 26 TGN 30 NGC 30 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
16 sample-a tumor-a G T 36 TGG 25 TGN 30 NGG 30 Gref |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
17 sample-a tumor-a T A 100 ATA 100 ATN 100 NTA 100 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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18 sample-a tumor-a T C 100 GTA 24 CTN 29 NTG 30 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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19 sample-a tumor-a T G 100 ATA 100 ATN 100 NTA 100 NA |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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20 |
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1cd1cf786389
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
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21 |