DiagnoseTargets two version conflict

arunprasarunpras san franciscoMember
edited January 2015 in Ask the GATK team

Hi.

I tried running DiagnoseTargets for the same BAM file using two versions of DiagnoseTargets and i see difference in results. Can you please help me with why this is happening. I see a lot of differences in the BAD_MATE filter. I have put in two sample intervals below

i used GATK 3.1-1-g07a4bf8 and GATK-lite v2.3.9-lite and default command line options


GATK-lite v2.3.9-lite output

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00109 HG00118 HG00134 HG00151 HG00152 HG00156 HG00176 HG00185 HG00237 HG00306 HG00335 HG00377 HG00378 HG00443 HG00452 HG00580 HG01075 NA18982 NA18992 NA19079 NA19116 NA19324 NA19346 NA19431 NA19456 NA19654 NA19664 NA19746 NA20525 NA20801

1 955543 . T

. LOW_MEDIAN_DEPTH AVG_INTERVAL_DP=408.03;END=955763 AVG_INTERVAL_DP:FT:MED:Q1:Q3 19.19:PASS:18.00:9.00:30.00 17.30:PASS:17.00:10.00:25.00 23.40:PASS:23.00:16.00:33.00 14.40:PASS:13.00:8.00:21.00 20.44:PASS:21.00:14.00:27.00 13.71:PASS:13.00:10.00:17.00 22.86:PASS:21.00:14.00:31.00 20.05:PASS:19.00:12.00:26.00 19.88:PASS:19.00:13.00:28.00 19.31:PASS:20.00:12.00:26.00 23.28:PASS:23.00:15.00:32.00 14.91:PASS:14.00:9.00:19.00 3.49:LOW_COVERAGE:4.00:3.00:4.00 7.13:LOW_COVERAGE:8.00:3.00:11.00 3.39:LOW_COVERAGE:4.00:2.00:4.00 8.02:PASS:8.00:5.00:10.00 6.35:LOW_COVERAGE:7.00:3.00:9.00 15.41:PASS:15.00:8.00:21.00 8.85:LOW_COVERAGE:9.00:4.00:13.00 14.95:PASS:15.00:9.00:21.00 16.41:PASS:17.00:7.00:25.00 10.30:LOW_COVERAGE:9.00:2.00:18.00 11.15:PASS:10.00:6.00:15.00 17.19:PASS:15.00:7.00:27.00 10.57:PASS:11.00:5.00:16.00 5.43:LOW_COVERAGE:5.00:2.00:8.00 7.21:BAD_MATE;LOW_COVERAGE:6.00:2.00:12.00 ** 11.43:PASS:12.00:5.00:17.00 **11.11:BAD_MATE:11.00:4.00:18.00 10.91:BAD_MATE:12.00:6.00:14.00

1 957571 . T

. PASS AVG_INTERVAL_DP=578.46;END=957852 AVG_INTERVAL_DP:FT:MED:Q1:Q3 15.64:PASS:15.00:10.00:22.00 _ 22.86:BAD_MATE:21.00:11.00:35.00_ 24.36:PASS:24.00:13.00:34.00 21.54:PASS:20.00:10.00:30.00 31.96:PASS:30.50:20.00:44.00 15.21:PASS:13.00:7.00:23.00 17.68:PASS:17.00:10.00:23.00 21.70:PASS:21.00:12.00:32.00 _19.06:BAD_MATE:18.00:11.00:25.00 17.14:BAD_MATE:15.00:7.00:26.00 _23.21:PASS:22.00:13.00:32.00 11.30:PASS:10.00:4.00:19.00 23.26:PASS:23.50:12.00:34.00 24.19:PASS:22.00:13.00:37.00 22.84:PASS:22.00:14.00:31.00 19.32:PASS:18.00:9.00:28.00 24.58:PASS:23.00:10.00:37.00 ** _15.92:BAD_MATE:15.00:9.00:22.00 _16.41:PASS:16.00:8.00:23.00 9.40:PASS:9.00:4.00:13.00 19.08:PASS:18.00:8.00:27.00 **_12.98:BAD_MATE:11.50:6.00:19.00 _13.06:PASS:13.00:9.00:17.00 15.40:PASS:14.00:8.00:22.00 13.66:PASS:13.00:8.00:19.00 _13.81:BAD_MATE:12.50:7.00:19.00 7.40:BAD_MATE:6.50:3.00:12.00 14.13:BAD_MATE:12.00:6.00:21.00_ 15.21:PASS:12.50:5.00:24.00 56.13:PASS:49.00:28.00:84.00

GATK 3.1-1-g07a4bf8 output

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00109 HG00118 HG00134 HG00151 HG00152 HG00156 HG00176 HG00185 HG00237 HG00306 HG00335 HG00377 HG00378 HG00443 HG00452 HG00580 HG01075 NA18982 NA18992 NA19079 NA19116 NA19324 NA19346 NA19431 NA19456 NA19654 NA19664 NA19746 NA20525 NA20801

1 955543 . T

. PASS END=955763;GC=0.751;IDP=407.84 FT:IDP:LL:ZL PASS:19.15:0:0 PASS:17.30:0:0 PASS:23.40:0:0 PASS:14.40:17:0 PASS:20.27:0:0 PASS:13.71:0:0 PASS:22.87:0:0 PASS:20.05:0:0 PASS:19.88:0:0 PASS:19.31:0:0 PASS:23.28:0:0 PASS:14.91:0:0 LOW_COVERAGE;POOR_QUALITY:3.49:108:0 LOW_COVERAGE:7.13:65:0 LOW_COVERAGE;POOR_QUALITY:3.39:106:0 PASS:8.02:0:0 LOW_COVERAGE:6.35:57:0 PASS:15.41:0:0 LOW_COVERAGE:8.85:51:0 PASS:14.95:0:0 PASS:16.41:0:0 LOW_COVERAGE:10.30:56:10 PASS:11.15:6:0 PASS:17.19:0:0 PASS:10.57:20:0 LOW_COVERAGE:5.43:74:0 LOW_COVERAGE:7.21:91:0 PASS:11.43:39:0 PASS:11.11:26:0 PASS:10.91:7:0

1 957571 . T

. PASS END=957852;GC=0.610;IDP=578.29 FT:IDP:LL:ZL PASS:15.64:10:0 PASS:22.86:15:4 PASS:24.36:14:0 PASS:21.54:20:10 PASS:31.96:11:0 PASS:15.21:19:0 PASS:17.68:19:0 PASS:21.70:8:8 PASS:19.06:8:11 PASS:17.14:14:11 PASS:23.21:25:0 PASS:11.30:41:5 PASS:23.26:11:0 PASS:24.19:30:0 PASS:22.84:8:0 PASS:19.32:30:0 PASS:24.58:25:0 PASS:15.92:7:4 PASS:16.41:13:0 PASS:9.40:43:7 PASS:18.96:27:4 PASS:12.98:37:3 PASS:13.00:21:0 PASS:15.40:13:7 PASS:13.66:11:0 PASS:13.81:19:0 POOR_QUALITY:7.40:32:19 PASS:14.15:27:9 PASS:15.21:26:0 PASS:56.13:11:0

These are the command lines:

GATK-lite v2.3.9-lite

fileformat=VCFv4.1
DiagnoseTargets="analysis_type=DiagnoseTargets input_file=[/sbgenomics/t46801.j412283.PrintReadsLite.work/Sample_group_unknown.base_recalibrated.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/sbgenomics/t46801.j607435.InputWrapper.execute/Projects/7608/TruSightOne.nochr.bed] excludeIntervals=null i
nterval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/sbgenomics/t46801.j512286.DiagnoseTargetsLite._work/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_leg
acy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT rem
ove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_leve
l=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub minimum_base_qualit
y=20 minimum_mapping_quality=5 minimum_coverage=5 maximum_coverage=1073741823 minimum_median_depth=10 maximum_insert_size=500 voting_status_threshold=0.5 low_median_depth_status_threshold=0.2 bad_mate_status_threshold=0.5 coverage_status_threshold=0.2 excessive_coverage_status_threshold=0.2 quality_status_threshold=0.5 print_debug_log=false filter

mismatching_base_and_quals=false"

GATK-lite v2.3.9-lite

GATKCommandLine=<ID=DiagnoseTargets,Version=3.1-1-g07a4bf8,Date="Mon Jan 05 01:46:53 EST 2015",Epoch=1420440413672,CommandLineOptions="analysis_type=DiagnoseTargets input_file=[_7_Sample_group_unknown.base_recalibrated.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[//Users/arun/Desktop/recombine_script/infile/TruSightOne.nochr.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=depthofcoverage.log help=false version=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub minimum_base_quality=20 minimum_mapping_quality=20 minimum_coverage=5 maximum_coverage=1073741823 maximum_insert_size=500 voting_status_threshold=0.5 bad_mate_status_threshold=0.5 coverage_status_threshold=0.2 excessive_coverage_status_threshold=0.2 quality_status_threshold=0.5 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

Thanks
Arun

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @arunpras‌

    Hi Arun,

    Can you try with the latest version of GATK? https://www.broadinstitute.org/gatk/download

    -Sheila

  • arunprasarunpras san franciscoMember

    Hi Sheila.

    This is the output with GATK 3.3 (The latest version you provided)

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00109 HG00118 HG00134 HG00151 HG00152 HG00156 HG00176 HG00185 HG00237 HG00306 HG00335 HG00377 HG00378 HG00443 HG00452 HG00580 HG01075 NA18982 NA18992 NA19079 NA19116 NA19324 NA19346 NA19431 NA19456 NA19654 NA19664 NA19746 NA20525 NA20801

    1 955543 . T

    . PASS END=955763;GC=0.751;IDP=407.84 FT:IDP:LL:ZL PASS:19.15:0:0 PASS:17.30:0:0 PASS:23.40:0:0 PASS:14.40:17:0 PASS:20.27:0:0 PASS:13.71:0:0 PASS:22.87:0:0 PASS:20.05:0:0 PASS:19.88:0:0 PASS:19.31:0:0 PASS:23.28:0:0 PASS:14.91:0:0 LOW_COVERAGE;POOR_QUALITY:3.49:108:0 LOW_COVERAGE:7.13:65:0 LOW_COVERAGE;POOR_QUALITY:3.39:106:0 PASS:8.02:0:0 LOW_COVERAGE:6.35:57:0 PASS:15.41:0:0 LOW_COVERAGE:8.85:51:0 PASS:14.95:0:0 PASS:16.41:0:0 LOW_COVERAGE:10.30:56:10 PASS:11.15:6:0 PASS:17.19:0:0 PASS:10.57:20:0 LOW_COVERAGE:5.43:74:0 LOW_COVERAGE:7.21:91:0 PASS:11.43:39:0 PASS:11.11:26:0 PASS:10.91:7:0

    1 957571 . T

    . PASS END=957852;GC=0.610;IDP=578.29 FT:IDP:LL:ZL PASS:15.64:10:0 PASS:22.86:15:4 PASS:24.36:14:0 PASS:21.54:20:10 PASS:31.96:11:0 PASS:15.21:19:0 PASS:17.68:19:0 PASS:21.70:8:8 PASS:19.06:8:11 PASS:17.14:14:11 PASS:23.21:25:0 PASS:11.30:41:5 PASS:23.26:11:0 PASS:24.19:30:0 PASS:22.84:8:0 PASS:19.32:30:0 PASS:24.58:25:0 PASS:15.92:7:4 PASS:16.41:13:0 PASS:9.40:43:7 PASS:18.96:27:4 PASS:12.98:37:3 PASS:13.00:21:0 PASS:15.40:13:7 PASS:13.66:11:0 PASS:13.81:19:0 POOR_QUALITY:7.40:32:19 PASS:14.15:27:9 PASS:15.21:26:0 PASS:56.13:11:0

    This again didn't have any BAD_MATES. Does this mean, there was a bug in the GATK lite version?

    Thanks
    Arun

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @arunpras‌

    Hi Arun,

    Yes, that is probably the case. GATK lite is very old, and we prefer users to use the latest version of GATK to get the best results.

    -Sheila

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