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how to use gatk to analysis multi samples at different tumor phase? GenotypeGVCFs or Mutect2

Hello, I am a fresh in gatk, I got some samples from different patient at different phase. for exmaple:
normal phase : 1 patient sample
tumor phase1 : 9 patient samples
tumor phase2 : 7 patient samples
tumor phase3 : 10 patient samples

I went to attain the specific variants at different phases, by reading the gatk best practice, I have finished joint calling to each phase (CombineGVCFs+GenotypeGVCFs) .

#samples is different phase sample
sample_gvcfs=""
for sample in $samples ; do 
    sample_gvcfs=${sample_gvcfs}"-V $outdir/${sample}/gatk/${sample}.HC.g.vcf.gz \\"\n
done
time $gatk CombineGVCFs \
    -R $reference/Homo_sapiens_assembly38.fasta \
    ${sample_gvcfs} \
    -O $outdir/population/${outname}.HC.g.vcf.gz && echo "** ${outname}.HC.g.vcf.gz done ** " && \
time $gatk GenotypeGVCFs \
    -R $reference/Homo_sapiens_assembly38.fasta \
    -V $outdir/population/${outname}.HC.g.vcf.gz \
    -O $outdir/population/${outname}.HC.vcf.gz && echo "** ${outname}.HC.vcf.gz done ** "

I get two questions following:

1.After getting vcf and using hard filter, I found there is still too much varients, how can I remove more unrelated variants ? (may be I can use normal sample to filter more varient, is there any tools?)

2.Mutect2 in gatk is the better choice in this situation ?

Any help will be appreciated !

Best Answer

Answers

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @javis In GATK 4.1 and later Mutect2 supports multiple tumor and normal samples from the same patient. You just run Mutect2 with a -I ____.bam for each sample and for the matched normal add -normal normal_sample_name, where the sample name is the @SM field in the BAM header. For more details you may refer to our documentation: https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf.

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