Which Manta output file one must consider in a joint tumor/normal SVs call?
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5 weeks ago
giusdalt95 • 0

Good Morning, I have successfully ran Manta on a couple of tumor/normal BAM files. It gave me 4 VCF files, but I am not sure of which one to use for my analyses. My aim is to analyze structural variants ONLY at tumor level, but the file "somatiSV.vcf.gz" misses some important informations, such as the genotype and the genotype quality, fields that are specified in the file "diploidSV.vcf.gz". Note that I have extensively analyzed the manual on github (https://github.com/Illumina/manta/tree/master/docs/userGuide#introduction), and I am writing here because i have not found a precise answer. Thank you in advance!

Structural Variants Manta • 96 views
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