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Picard CollectOxoGMetrics empty metrics

Zhenyu_ZhangZhenyu_Zhang University of ChicagoMember
edited February 2017 in Ask the GATK team

I tried to collect OxoG metrics, but less than 2% of my BAMs gave empty metrics as below. I have also updated my picard to 2.8.3. The example file I have is of normal size (14G). Also I saw from another thread asking about read group information, and it does.

@RG ID:0    CN:BCM  DS:Wilms Tumor PI R Gibbs   DT:2012-05-31T12:00:00+0000 LB:ING_WTSRG.PAKGZX01A-1_1pA    PL:Illumina PU:110208_SN601_0075_A81K6MABXX_6   SM:TARGET-50-PAKGZX-01A-01D
## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectOxoGMetrics INPUT=TARGET-50-PAKGZX-01A-01D_hg19_Illumina_gdc_realn.bam OUTPUT=temp REFERENCE_SEQUENCE=/home/ubuntu/SCRATCH/GRCh38.d1.vd1.fa    MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=tr
ue 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 GA4GH_CLIENT_SECRETS=client_secrets.json
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Feb 20 18:44:42 UTC 2017

## 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
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   CCA 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   ACC 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   CCC 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   GCA 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   TCT 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   ACG 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   CCG 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   GCC 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   GCG 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   ACT 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   TCA 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   CCT 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   TCC 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   GCT 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   TCG 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
TARGET-50-PAKGZX-01A-01D    ING_WTSRG.PAKGZX01A-1_1pA   ACA 0   0   0   0   0   0   0   ?   -?  0   0   0   0   ?   ?   ?   ?
Post edited by shlee on

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by Sheila

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