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

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582

## 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