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Mutect2 output with samples with different read groups

Hi all,
I am running Mutect2 with a tumour/normal match in RNA-Seq. Here is my command:

gatk -T MuTect2 -R ./genome.fa --read_filter Mappin
gQuality --min_mapping_quality_score 20 --max_alternate_alleles 4 -kmerSize 15 -kmerSize 30 -I:tumor ./9_Recal.reorderedDupl.rg.split.bam -I:normal ./8_Recal.reorderedDupl.rg.split.bam --dbsnp ./dbsnp_144.hg38.vcf.gz -L ./genes_for_variant_calling.bed -o ./9_somatic_snvs_indels.vcf -log ./9_somatic_snvs_indels_log

In the output (I am showing here output opened in R with the VariantAnnotation package) I get the following data for the genotypes:

                                        8_L003       8_L004     8_L007     8_L008        9_L003     9_L004       9_L007    9_L008

chr1:36466762_A/G "0/0" "." "." "." "0/1" "." "." "."
chr1:36468081_A/G "0/0" "." "." "." "0/1" "." "." "."
chr1:36475819_A/G "0/0" "." "." "." "0/1" "." "." "."
chr1:36476164_A/G "0/0" "." "." "." "0/1" "." "." "."
chr1:36476671_C/CT "0/0" "." "." "." "0/1" "." "." "."
chr1:36476745_T/C "0/0" "." "." "." "0/1" "." "." "."

I get the same strange output for many other samples. It is like the variants are found in a subset of reads related to one one read group. All the variants are like this. Shall I get really worried about my data or Mutect2 does some comparisons that I am not aware of?

Thanks for your help,

Anna

Answers

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