There have wrong AP/DP output in the --vcf output for the mutect.1.1.4.jar

Dragon_fireDragon_fire chinaMember
edited August 2015 in Ask the GATK team

we specified --vcf output for using the the mutect.1.1.4.jar and the mutect.1.1.1.jar, the 1.1.1 version displayed it didn't define the vcf parameter, the 1.1.4 version had complete vcf result, but we found its the AP/DP column result is as the same as the sum of quality scores of reference/alternate alleles in tumor of metect default output. Could you tell me the reasons ? Thanks very much.

we find mutect.1.1.7 version in this forum and ready to try this version.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    I'm not sure I understand the problem. Can you post some lines from the output showing the problem? Also, be sure to try the 1.1.7 version.

  • Dragon_fireDragon_fire chinaMember
    edited August 2015

    the part of --vcf output result is :

    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  RCC165
    chr1    866319  rs9988021       G       A       .       REJECT  DB      GT:AD:BQ:DP:FA  0:0,28:.:28:1.00
    chr1    870903  rs13303094      T       C       .       REJECT  DB      GT:AD:BQ:DP:FA  0:0,7:.:7:1.00
    

    the corresponding --out default output is :

    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
    chr1    866319  AGCxGGG G   A   sample  sample  0   DBSNP   COVERED 0.457242    0.457757    0.998875    52  0   0   85.589489   1   0.0 -0.192977   0   22  0   751 0   60  0   0   AA  -108.250672 0   28  0   949 REJECT
    chr1    870903  ACAxAGA T   C   RCC165  RCC165  0   DBSNP   UNCOVERED   0   0.043787    0   14  0   0   27.838523   1   0.02    -0.061408   0   7   0   245 0   60  0   0   CC  -28.544977  0   7   0   252 REJECT
    

    Through reading the header information, the AP reslult in --vcf output should be the same as t_ref_count/t_alt_count in --out output.
    But comparing the two types of output, we find :For chr1-866319 site , the AP reslult in --vcf output is 0,28 as the same as the n_ref_count/n_alt_count in --out output (Mutect Default output). this situation also have happened in other mutation site.

    My Mutect command lines is :

    java -Xmx2G -Djava.io.tmpdir=java_tmp -jar muTect-1.1.4.jar --analysis_type MuTect --reference_sequence hg19.fasta --cosmic hg19_cosmic_v62_291112.vcf --dbsnp dbsnp_132_b37.leftAligned.format.vcf  --intervals ex_region.sort.bed --input_file:normal sample-normal.bam --input_file:tumor sample-tumor.bam --out sample.mutect.out --coverage_file sample.mutect.coverage --vcf sample.mutect.vcf && \
    
  • Thanks, i have found the reasons that the header of tumor and normal sample BAM files have same sample name.

    @Geraldine_VdAuwera said:
    I'm not sure I understand the problem. Can you post some lines from the output showing the problem? Also, be sure to try the 1.1.7 version.

Sign In or Register to comment.