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comparison test-data/pre_summary @ 23:1cd1cf786389 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
author iuc
date Thu, 16 May 2019 07:13:32 -0400
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children 3f254c5ced1d
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22:f6ced08779c4 23:1cd1cf786389
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
3 ## htsjdk.samtools.metrics.StringHeader
4 # Started on: Fri May 03 21:58:49 EDT 2019
5
6 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterSummaryMetrics
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 100 CAC 31 CAN 36 NAC 35 NA
9 sample-a tumor-a A G 100 GAG 28 GAN 33 NAG 31 NA
10 sample-a tumor-a A T 100 AAA 100 AAN 100 NAA 100 NA
11 sample-a tumor-a C A 39 CCA 27 CCN 33 NCA 33 NA
12 sample-a tumor-a C G 100 ACA 100 ACN 100 NCA 100 NA
13 sample-a tumor-a C T 100 GCT 27 GCN 33 NCT 33 Deamination
14 sample-a tumor-a G A 42 CGA 27 CGN 33 NGA 31 NA
15 sample-a tumor-a G C 39 TGC 29 TGN 33 NGC 33 NA
16 sample-a tumor-a G T 100 AGA 100 AGN 100 NGA 100 OxoG
17 sample-a tumor-a T A 100 ATA 100 ATN 100 NTA 100 NA
18 sample-a tumor-a T C 27 ATA 19 ATN 23 NTA 22 NA
19 sample-a tumor-a T G 100 TTA 30 TTN 35 NTA 37 NA
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