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dakl/oxog.txt

Last active February 10, 2016 13:26
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oxog.txt
## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectOxoGMetrics INPUT=virtual-tumor.bam OUTPUT=oxog.txt REFERENCE_SEQUENCE=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Feb 10 11:23:36 UTC 2016
## METRICS CLASS picard.analysis.CollectOxoGMetrics$CpcgMetrics
SAMPLE_ALIAS LIBRARY CONTEXT TOTAL_SITES TOTAL_BASES REF_NONOXO_BASES REF_OXO_BASES REF_TOTAL_BASES ALT_NONOXO_BASES ALT_OXO_BASES OXIDATION_ERROR_RATE OXIDATION_Q C_REF_REF_BASES G_REF_REF_BASES C_REF_ALT_BASES G_REF_ALT_BASES C_REF_OXO_ERROR_RATE C_REF_OXO_Q G_REF_OXO_ERROR_RATE G_REF_OXO_Q
virtual-tumor virtual-tumor ACT 27 388 238 150 388 0 0 0.002577 25.888317 162 226 0 0 0 100 0 100
virtual-tumor virtual-tumor GCT 13 313 170 143 313 0 0 0.003195 24.955443 133 180 0 0 0 100 0 100
virtual-tumor virtual-tumor CCA 19 295 133 162 295 0 0 0.00339 24.69822 22 273 0 0 0 100 0 100
virtual-tumor virtual-tumor TCT 42 1039 457 582 1039 0 0 0.000962 30.166155 679 360 0 0 0 100 0 100
virtual-tumor virtual-tumor CCC 7 21 16 5 21 0 0 0.047619 13.222193 1 20 0 0 0 100 0 100
virtual-tumor virtual-tumor ACA 30 572 303 269 572 0 0 0.001748 27.57396 354 218 0 0 0 100 0 100
virtual-tumor virtual-tumor CCG 1 1 0 1 1 0 0 1 -0 0 1 0 0 ? ? ? ?
virtual-tumor virtual-tumor ACC 14 172 91 81 172 0 0 0.005814 22.355284 27 145 0 0 0 100 0 100
virtual-tumor virtual-tumor GCG 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
virtual-tumor virtual-tumor TCG 1 48 34 14 48 0 0 0.020833 16.812412 0 48 0 0 ? ? ? ?
virtual-tumor virtual-tumor ACG 3 46 14 32 46 0 0 0.021739 16.627578 46 0 0 0 ? ? ? ?
virtual-tumor virtual-tumor TCA 27 535 273 262 535 0 0 0.001869 27.283538 219 316 0 0 0 100 0 100
virtual-tumor virtual-tumor GCC 3 45 22 23 45 0 0 0.022222 16.532125 20 25 0 0 0 100 0 100
virtual-tumor virtual-tumor CCT 13 292 172 120 292 0 0 0.003425 24.653829 127 165 0 0 0 100 0 100
virtual-tumor virtual-tumor TCC 15 371 189 181 370 0 1 0.002695 25.693739 104 266 0 1 0 100 0.003745 24.265113
virtual-tumor virtual-tumor GCA 19 346 161 185 346 0 0 0.00289 25.390761 199 147 0 0 0 100 0 100
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