Germline indels not detected by strelka2 and samtools/VarScan · Biostar

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Germline indels not detected by strelka2 and samtools/VarScan

Hello everyone. I'm trying to detect indels using strelka2 and samtools/VarScan. The problem is: I have used GATK 4.0 with default options and he could detect the deletion. Is a 41bp deletion which is confirmed by MLPA but, couldn't detect using strelka2 and samtools/VarScan. For Sk and SV, I've used default parameters. So, does anyone know if SK and SV have any limitation on indel size calling?

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written 6.8 years ago by brunobsouzaa

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