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Stop in Mutect2 running on an early phase

suhyesuhye SouthKoreaMember

Hello, GATK team
I have some problems with running Mutect2

I have some sample aligned hg19 (including chrM, 1-22, X, Y) reference genome
and I did run mutect2 with these samples (normal and tumor, also)

but when I checked output vcf files, only I could see variants on chrM and chr1

so, I did re-run mutect2 and stopping situation in mutect2 running on chromosome 1 early phase and that look like just end of analysis procedure (no error message, no warning message)

I attached captured image about this situation

How can i solve this?

Best Answer


  • suhyesuhye SouthKoreaMember

    @SChaluvadi Hello, SChaluvadi
    Sure. This is the exact command i run

    • gatk --java-options "-Xmx16g" Mutect2 -R UCSC_hg19_nocontig.fa --germline-resource GATKbundle/dbsnp_138.hg19.excluding_sites_after_129_nocontig_sorted.vcf -I $BAM_DIR/$N_hg19.bam -I $BAM_DIR/$T_hg19.bam -normal $N -tumor $T -O $MT_DIR/$name.vcf

    • and i used these tool "BWA-mem", "GATK", "samtools" for alignment and post-processing of alignment files

    I didn't use any interval file, and samples were made by WES sequencing

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @suhye The problem is that you are using a dbsnp file that does not have an AF in the info field as your germline resource. You can replace that one with this: our best practices gnomAD instead - gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf

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