Mercurial > repos > devteam > picard
annotate test-data/pos_summary @ 28:c943f4a04af0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
| author | iuc |
|---|---|
| date | Mon, 25 Sep 2023 08:31:14 +0000 |
| parents | f8748e3fd865 |
| children |
| rev | line source |
|---|---|
|
18
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
1 ## htsjdk.samtools.metrics.StringHeader |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
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 |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
3 ## htsjdk.samtools.metrics.StringHeader |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
4 # Started on: Fri May 03 21:58:49 EDT 2019 |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
5 |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
6 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasSummaryMetrics |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
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 |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
8 sample-a tumor-a A C 35 TAA 26 CAN 34 NAA 28 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
9 sample-a tumor-a A G 16 TAT 9 TAN 11 NAT 12 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
10 sample-a tumor-a A T 100 AAA 100 AAN 100 NAA 100 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
11 sample-a tumor-a C A 100 ACA 100 ACN 100 NCA 100 Cref |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
12 sample-a tumor-a C G 100 ACA 100 ACN 100 NCA 100 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
13 sample-a tumor-a C T 100 TCA 29 ACN 100 NCA 34 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
14 sample-a tumor-a G A 34 CGA 23 AGN 28 NGA 30 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
15 sample-a tumor-a G C 36 TGC 26 TGN 30 NGC 30 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
16 sample-a tumor-a G T 36 TGG 25 TGN 30 NGG 30 Gref |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
17 sample-a tumor-a T A 100 ATA 100 ATN 100 NTA 100 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
18 sample-a tumor-a T C 100 GTA 24 CTN 29 NTG 30 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
19 sample-a tumor-a T G 100 ATA 100 ATN 100 NTA 100 NA |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
20 |
|
f8748e3fd865
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff
changeset
|
21 |