Question

GenomicsDBImport from Mutect2 output

1

Entering edit mode

2.8 years ago

cocchi.e89 ▴ 270

I am trying to follow GATK 4.2.0 best-practice guidelines for Mutect2 PoN creation. I called variants in my samples as recommended with:

gatk Mutect2 \
    -R ${REF} \
    -L ${EXOME_INPUT_INTERVALS} \
    -I ${BAM} \
    --sequence-dictionary ${DICT} \
    --max-mnp-distance 0 \
    -O ${SAMPLE_NAME}.mutect2.vcf

but I see that the tool is unable to create a proper GenomicsDB through the GenomicsDBImport command. Even focusing the analysis on a little interval in which I know I have variants in the Mutect2 generated VCFs, here the SelectVariants output from one of the VCF I'll use in the GenomicsDBImport command:

 #CHROM POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  XXX
 1  883625  .   A   G   .   .   AS_SB_TABLE=0,0|12,41;DP=54;ECNT=1;MBQ=0,33;MFRL=0,260;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=182.40 GT:AD:AF:DP:F1R2:F2R1:SB    0/1:0,53:0.981:53:0,26:0,26:0,0,12,41

and here the command to generate the DB:

gatk \
    --java-options "-Djava.io.tmpdir=/nfs/projects/CNV_WGS/CHIP-PON-DB/TMP-DIR" \
      GenomicsDBImport \
      -R $REF \
      -L 1:883600-883650 \
      --genomicsdb-workspace-path $OUT \
      --tmp-dir /nfs/projects/CNV_WGS/CHIP-PON-DB/TMP-DIR \
      -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0003D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0020D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0008D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq48f19.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq138f52.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0052D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0019D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0051D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq186f69.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq126f48.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq303f113.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq251f92.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq319f119.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/neuro221f102.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq382f144.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0084D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0096D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0075D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq509f190.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq537f200.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0082D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0068D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq665f245.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq673f249.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0113D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0126D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0114D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/neuro551f306.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq575f215.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq879f322.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq917f335.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq920f336.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0146D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0148D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0147D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0151D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1070f254.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1000f365.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1092f397.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1098f399.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1102f400.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0155D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0165D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1239f446.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/neuro989f551.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0214D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0217D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0221D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1703f610.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1153f417.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1383f497.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1388f499.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1394f501.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1413f507.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1438f516.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1508f540.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1741f622.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq1746f624.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0159D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0166D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0169D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0170D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0173D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0175D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0182D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0192D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0193D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0197D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0202D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0206D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0210D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/neuro1089f613.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/neuro741f416.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/ocd4005001236yy3.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/fetal0015D.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq264f96.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq436f163.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/neuro337f175.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq530f196.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq608f226.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq621f231.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq639f237.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/neuro442f249.Roche-M.mutect2.vcf -V /nfs/projects/CNV_WGS/Mutetc2-PON-OUT/Roche-M/diagseq944f346.Roche-M.mutect2.vcf

I get an EMPTY GenomicsDB!!!

gatk SelectVariants   --java-options "-Djava.io.tmpdir=/nfs/projects/CNV_WGS/CHIP-PON-DB/TMP-DIR" \
    -R $REF 
    -V gendb://$OUT \
    -L 1:883600-883650 \
    -O output.chr1_883600_883650.vcf

### OUTPUT: empty VCF (only header)

Does anybody had this problem before or have a clue why? I'm losing my mind! I also googled and searched around and found similar issues like this but none explained why this should happen with my data!

Mutect2 GenomicsDBImport somatic VCF GATK • 1.1k views

ADD COMMENT • link updated 10 months ago by sure ▴ 100 • written 2.8 years ago by cocchi.e89 ▴ 270

0

Entering edit mode

@ccchi.e89 Hi did you manage to figure out, why your were getting empty output following GenomicsDBImport commmand. I am facing the same issue and was hoping to get your insight into it.

ADD REPLY • link 10 months ago by sure ▴ 100