User: Thomas Sandmann

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3 years, 10 months ago
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4 years, 7 months ago
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Posts by Thomas Sandmann

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ensemblVEP, variant_effect_predictor versions and release schedule
... Hi Valerie, thanks a lot for supporting legacy versions of the ensembl database / variant_effect_predictor.pl script. I assume you're still using version 67 and have the data cached. Yes, that's right. We use ensembl release 67 together with the corresponding variant_effect_predictor.pl script ...
transcription hapmap polyphen sift convert genomes ensemblvep written 3.9 years ago by Thomas Sandmann30 • updated 3.9 years ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: ensemblVEP: passing on coverage / frequency information
... Thanks for fixing the functions so quickly. That helps a lot ! Thomas [[alternative HTML version deleted]] ...
written 4.6 years ago by Thomas Sandmann30
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Comment: C: ensemblVEP: passing on coverage / frequency information
... Hi Valerie, thanks a lot for looking following up on this issue. Yes, I generated the input for ensemblVEP with a call to writeVcf. Here's my workflow: 1. Variant calling with the '*callVariants*' function from the '* VariantTools*' package: returns the* 'variants.gr' GRanges object* 2. Generate ...
written 4.6 years ago by Thomas Sandmann30

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