view test-data/err_summary @ 26:9ffcddf6f9c0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit cbe534af56ee782e8d1aa0fa872059d2a5e42db8"
author iuc
date Mon, 17 Feb 2020 10:24:29 -0500
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.ErrorSummaryMetrics
REF_BASE	ALT_BASE	SUBSTITUTION	REF_COUNT	ALT_COUNT	SUBSTITUTION_RATE
A	C	A>C	3877	0	0
A	G	A>G	3877	2	0.000516
A	T	A>T	3877	0	0