Mercurial > repos > devteam > picard
comparison test-data/pos_summary @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | 1cd1cf786389 |
| children |
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| 32:f9242e01365a | 33:3f254c5ced1d |
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| 1 ## htsjdk.samtools.metrics.StringHeader | 1 ## htsjdk.samtools.metrics.StringHeader |
| 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 | 2 # CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=picard_ARRG_test1_bam OUTPUT=OutPut ASSUME_SORTED=false VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/home/bag/projects/code/tools-iuc/tools/picard/test-data/cached_locally/picard_BedToIntervalList_ref.fa INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false |
| 3 ## htsjdk.samtools.metrics.StringHeader | 3 ## htsjdk.samtools.metrics.StringHeader |
| 4 # Started on: Fri May 03 21:58:49 EDT 2019 | 4 # Started on: Sat Mar 02 14:48:33 GMT 2024 |
| 5 | 5 |
| 6 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasSummaryMetrics | 6 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasSummaryMetrics |
| 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 | 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 |
| 8 sample-a tumor-a A C 35 TAA 26 CAN 34 NAA 28 NA | 8 sample-a tumor-a A C 35 TAA 26 CAN 34 NAA 28 NA |
| 9 sample-a tumor-a A G 16 TAT 9 TAN 11 NAT 12 NA | 9 sample-a tumor-a A G 16 TAT 9 TAN 11 NAT 12 NA |