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New VEP does not handle Delly SV VCFs #208

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ckandoth opened this issue Dec 26, 2018 · 0 comments
Open

New VEP does not handle Delly SV VCFs #208

ckandoth opened this issue Dec 26, 2018 · 0 comments
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The older VEP v86 and v88 seem to work fine with vcf2maf v1.6.15 and generate a proper MAF for the SVs. But VEP v92 with vcf2maf 1.6.16 produces an empty MAF. Most likely because the newer VEP handles ALT=<SV_TYPE> format differently.
@ckandoth ckandoth self-assigned this Dec 26, 2018
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