Mercurial > repos > devteam > picard
view test-data/pre_summary @ 32:f9242e01365a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author | iuc |
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date | Mon, 25 Sep 2023 08:32:17 +0000 |
parents | 1cd1cf786389 |
children | 3f254c5ced1d |
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## htsjdk.samtools.metrics.StringHeader # 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 ## htsjdk.samtools.metrics.StringHeader # Started on: Fri May 03 21:58:49 EDT 2019 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterSummaryMetrics 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 sample-a tumor-a A C 100 CAC 31 CAN 36 NAC 35 NA sample-a tumor-a A G 100 GAG 28 GAN 33 NAG 31 NA sample-a tumor-a A T 100 AAA 100 AAN 100 NAA 100 NA sample-a tumor-a C A 39 CCA 27 CCN 33 NCA 33 NA sample-a tumor-a C G 100 ACA 100 ACN 100 NCA 100 NA sample-a tumor-a C T 100 GCT 27 GCN 33 NCT 33 Deamination sample-a tumor-a G A 42 CGA 27 CGN 33 NGA 31 NA sample-a tumor-a G C 39 TGC 29 TGN 33 NGC 33 NA sample-a tumor-a G T 100 AGA 100 AGN 100 NGA 100 OxoG sample-a tumor-a T A 100 ATA 100 ATN 100 NTA 100 NA sample-a tumor-a T C 27 ATA 19 ATN 23 NTA 22 NA sample-a tumor-a T G 100 TTA 30 TTN 35 NTA 37 NA