Why the candidate like this is rejected? It seems to meet all requirements.

HangHang Hong KongMember
edited August 2016 in MuTect v1
contig  position    context ref_allele  alt_allele  tumor_name  normal_name score   dbsnp_site  covered power   tumor_power normal_power    total_pairs improper_pairs  map_Q0_reads    t_lod_fstar tumor_f contaminant_fraction    contaminant_lod t_ref_count t_alt_count t_ref_sum   t_alt_sum   t_ref_max_mapq  t_alt_max_mapq  t_ins_count t_del_count normal_best_gt  init_n_lod  n_ref_count n_alt_count n_ref_sum   n_alt_sum   judgement
4   46979366    AAGxAAG     A   G   Tumor   Normal  0   DBSNP   COVERED 0.858553    0.865745    0.991692    106 2   0   47.881231   0.515152    0.02    -0.342024   16  17  471 497 60  60  0   23  AA  7.516792    25  0   804 0   REJECT
Post edited by Geraldine_VdAuwera on
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by Sheila

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Answers

  • chenlilianchenlilian ChinaMember

    @Geraldine_VdAuwera, I have the same question like this one. I have checked the parameters showed in http://gatkforums.broadinstitute.org/gatk/discussion/4464/how-mutect-filters-candidate-mutations, there is some sites meet all the cutoffs when i check the stats file, but they are not showed in mutect.vcf. Can you give some detail about the updated parameters used to define which sites should show in the final vcf?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Can you please post some example records?
  • chenlilianchenlilian ChinaMember

    contig position context ref_allele alt_allele tumor_name normal_name score dbsnp_site covered power tumor_power normal_power normal_power_nsp normal_power_wsp total_reads map_Q0_reads init_t_lod t_lod_fstar t_lod_fstar_forward t_lod_fstar_reverse tumor_f contaminant_fraction contaminant_lod t_q20_count t_ref_count t_alt_count t_ref_sum t_alt_sum t_ref_max_mapq t_alt_max_mapq t_ins_count t_del_count normal_best_gt init_n_lod normal_f n_q20_count n_ref_count n_alt_count n_ref_sum n_alt_sum power_to_detect_positive_strand_artifact power_to_detect_negative_strand_artifact strand_bias_counts tumor_alt_fpir_median tumor_alt_fpir_mad tumor_alt_rpir_median tumor_alt_rpir_mad observed_in_normals_count failure_reasons judgement
    chr17 37879542 CCCxCAA T A tumor normal 0 DBSNP COVERED 1 1 1 1 1 2400 0 -542.704457 -2.176801 13.649941 0 0.018537 0.02 -1.412541 1084 2012 38 53695 535 60 60 0 0 TT 67.157802 0.037671 245 281 11 9460 154 0.999999 0.999997 (1169,1364,55,0) 52 13.5 22.5 10.5 0 fstar_tumor_lod,possible_contamination,alt_allele_in_normal,strand_artifact REJECT
    chr17 37858446 CTCxGGA C G tumor normal 0 DBSNP COVERED 1 1 1 1 1 3743 1 -932.433733 0.796995 1.354391 -0.415992 0.001271 0.02 3.0615 2243 3144 4 94486 103 60 60 0 0 CC 172.680769 0 559 574 0 20573 0 0.098482 0.107158 (1998,1798,13,1) 16 9 59 9 0 fstar_tumor_lod,possible_contamination REJECT
    chr3 178919413 TTTxGAG T G tumor normal 0 NOVEL COVERED 1 1 1 1 1 1696 10 -420.881654 0.927982 0 4.005899 0.005424 0.02 3.379451 648 1467 8 35132 166 60 60 1 0 TT 32.207056 0 107 107 0 3954 0 0.820566 0.570403 (710,1276,0,19) 63.5 10 11.5 10 0 fstar_tumor_lod,possible_contamination REJECT
    chr7 55271396 CACxACA C A tumor normal 0 NOVEL COVERED 1 1 1 1 1 2989 5 -548.308324 3.248948 4.038688 0.875956 0.018571 0.02 3.088533 1463 2061 39 52082 617 60 60 0 3 CC 82.572526 0.031977 258 333 11 10281 154 1 0.999997 (1175,1517,29,24) 39 11 28 12 0 fstar_tumor_lod,nearby_gap_events,possible_contamination,alt_allele_in_normal,strand_artifact REJECT

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    These sites all have annotations that tell you what filters they failed. Which of these is not clear?
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