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'