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loss some allele variants in final result whien analysisMode=FULL #578

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ArsFc opened this issue Nov 15, 2024 · 3 comments
Open

loss some allele variants in final result whien analysisMode=FULL #578

ArsFc opened this issue Nov 15, 2024 · 3 comments

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@ArsFc
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ArsFc commented Nov 15, 2024

approximately 1% variants can not find in final result

@ArsFc
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ArsFc commented Nov 15, 2024

from the logs during the run , some variants missing because 2024-11-15T07:51:51.039Z INFO 3569330 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Processed 152553 variant records into 151746 single allele variants (including 0 structural variants) ..

@julesjacobsen
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Sorry about the late reply - some variant in scaffold and unplaced regions will not be annotated or assessed, in addition variants which are homozygous ref (0/0) for the proband will not be assessed, even if analysisMode=FULL has been used.

Were you trying to use Exomiser to annotate the variants from a VCF for further downstream analysis?

@ArsFc
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ArsFc commented Jan 17, 2025

Sorry about the late reply - some variant in scaffold and unplaced regions will not be annotated or assessed, in addition variants which are homozygous ref (0/0) for the proband will not be assessed, even if analysisMode=FULL has been used.

Were you trying to use Exomiser to annotate the variants from a VCF for further downstream analysis?

yes , for rapid screening pathogenic variants

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