Tag: MuTect

What sequencing/alignment artifact is this?

What sequencing/alignment artifact is this? 0 I’m calling mitochondria variants with mutect2 and one variant looks like an artifact but I don’t understand what could be the cause. It looks like from IGV (picture below) that this variant is always at the same position on forward and backward reads. Also…

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Genetic characteristics involving the PD-1/PD-L1/L2 and CD73/A2aR axes and the immunosuppressive microenvironment in DLBCL

Key messages What is already known on this topic Targeting immunosuppressive pathways have emerged as promising strategies for cancer treatment. The genetic characteristics of PD-1/PD-L1/L2 (programmed cell death protein 1/programmed cell death ligand 1/ligand 2) and CD73/A2aR (A2a adenosine receptor) and the effect of these two signalings on dysfunctional CD8+…

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Bowtie2 hg19 reference for gatk MuTect

Bowtie2 hg19 reference for gatk MuTect 3 Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 as the aligner, which reference file should I be using? The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2 and…

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