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AD different with DP

Dear all,
I use this comand and version of mutect:

GATKCommandLine=<ID=MuTect,Version=3.1-0-g72492bb,Date="Fri Feb 03 13

:47:15 CET 2017",Epoch=1486126035093,CommandLineOptions="analysis_type=
MuTect input_file=[ALIGN/411/Coclean/412.sorted.dup.recal.cleaned.bam,
ALIGN/411/Coclean/411.sorted.dup.recal.cleaned.bam] showFullBamList=fal
se read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filte
r=[] intervals=[/illumina/software/database/database_2016/TARGET/truseq
-exome-targeted-regions-manifest-v1-2.bed] excludeIntervals=null interv
al_set_rule=UNION interval_merging=ALL interval_padding=0 reference_seq
uence=/illumina/software/database/database_2016/hg19_primary.fa nonDete
rministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRunti
meUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null down
sample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_q
uality_scores=false allow_potentially_misencoded_quality_scores=false u
seOriginalQualities=false defaultBaseQualities=-1 performanceLog=null B
QSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals
=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_s
trictness=LENIENT remove_program_records=false keep_program_records=fal
se sample_rename_mapping_file=null unsafe=null disable_auto_index_creat
ion_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_p
er_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam
file_handles=null read_group_black_list=null pedigree=[] pedigreeStrin
g=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=f
alse generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_in
dex_parameter=-1 logging_level=INFO log_to_file=null help=false version
=false noop=false enable_extended_output=false enable_qscore_output=fal
se artifact_detection_mode=false tumor_sample_name=411 bam_tumor_sample
_name=null normal_sample_name=412 force_output=false force_alleles=fals
e only_passing_calls=false initial_tumor_lod=4.0 tumor_lod=6.3 fraction
_contamination=0.02 minimum_mutation_cell_fraction=0.0 normal_lod=2.2 n
ormal_artifact_lod=1.0 strand_artifact_lod=2.0 strand_artifact_power_th
reshold=0.9 dbsnp_normal_lod=5.5 minimum_normal_allele_fraction=0.0 tum
or_f_pretest=0.005 min_qscore=5 gap_events_threshold=3 heavily_clipped

read_fraction=0.3 fraction_mapq0_threshold=0.5 pir_median_threshold=10.
0 pir_mad_threshold=3.0 required_maximum_alt_allele_mapping_quality_sco
re=20 max_alt_alleles_in_normal_count=2 max_alt_alleles_in_normal_qscor
e_sum=20 max_alt_allele_in_normal_fraction=0.03 power_constant_qscore=3
0 power_constant_af=0.30000001192092896 vcf=org.broadinstitute.sting.ga
tk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinst
itute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broad
institute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadins
titute.sting.gatk.io.stubs.VariantContextWriterStub dbsnp=[(RodBinding
name=dbsnp source=/illumina/software/Mutect_db/dbsnp_137.hg19.vcf.gz)]
cosmic=[] normal_panel=[] coverage_file=null coverage_20_q20_file=null
power_file=null tumor_depth_file=null normal_depth_file=null filter_rea
ds_with_N_cigar=false filter_mismatching_base_and_quals=false filter_ba
ses_not_stored=false">

INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">

INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality

Zero Reads">

INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic event">

INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SN

P, INS or DEL">

I have many REJECTED and where I have PASS I have on tumor column this strange results betwen AD vs DP

['58', '0'] 30
['60', '1'] 31
['78', '0'] 67
['104', '0'] 95
['164', '0'] 173
['11', '0'] 5

chrM', '14940', '.', 'T', 'C', '.', 'PASS', 'SOMATIC;VT=SNP', 'GT:AD:BQ:DP:FA:SS', '0:11,0:.:11:0.00:0', '0/1:0,5:33:5:1.00:2'

Tagged:

Issue · Github
by Sheila

Issue Number
1825
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Best Answer

Answers

  • Yes I use the last version of mutect1 (mutect-1.1.7.jar)

    The mutect2 not work need more than 7 day...

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    It's possible that these inconsistent counts are either due to different ways of filtering reads when calculating AD vs DP, or to some bug in the program. Unfortunately because Mutect1 is based on an older version of GATK, we aren't able to provide full support for it. Your best bet is to look at a few of the sites in the original data and determine whether the calls make sense or not.

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