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comparison test-data/pos_details @ 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$BaitBiasDetailMetrics
7 SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE CONTEXT FWD_CXT_REF_BASES FWD_CXT_ALT_BASES REV_CXT_REF_BASES REV_CXT_ALT_BASES FWD_ERROR_RATE REV_ERROR_RATE ERROR_RATE QSCORE
8 sample-a tumor-a A C AAA 58 0 857 0 0 0 0 100
9 sample-a tumor-a A C AAC 234 0 139 0 0 0 0 100
10 sample-a tumor-a A C AAG 52 0 265 0 0 0 0 100
11 sample-a tumor-a A C AAT 240 0 1358 0 0 0 0 100
12 sample-a tumor-a A C CAA 101 0 573 0 0 0 0 100
13 sample-a tumor-a A G AAA 58 0 857 1 0 0.001166 0 100
14 sample-a tumor-a A G AAC 234 1 139 0 0.004255 0 0.004255 24
15 sample-a tumor-a A G AAG 52 0 265 0 0 0 0 100
16 sample-a tumor-a A G AAT 240 0 1358 0 0 0 0 100
17 sample-a tumor-a A G CAA 101 0 573 0 0 0 0 100
18 sample-a tumor-a A T AAA 58 0 857 0 0 0 0 100
19 sample-a tumor-a A T AAC 234 0 139 0 0 0 0 100
20 sample-a tumor-a A T AAG 52 0 265 0 0 0 0 100
21 sample-a tumor-a A T AAT 240 0 1358 0 0 0 0 100
22 sample-a tumor-a A T CAA 101 0 573 0 0 0 0 100
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