User: romain.coppee

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Posts by romain.coppee

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Answer: A: GATK VariantFiltration does not filter
... Thank you for your reply ;) Harold, the PASS was due to another filter. However, I understood my problem. The annotation was correctly made with VariantFiltration, but the next step was to apply the filtering (and I did not perform it). For this, I used the following GATK command : gatk Sele ...
written 12 days ago by romain.coppee0
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Comment: C: GATK VariantFiltration does not filter
... Hi, thanks for your reply. The name of my filter is wrong, you're right; but even if I execute the command as you propose, there is no difference, any variants were filtered. ...
written 13 days ago by romain.coppee0
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GATK VariantFiltration does not filter [SOLVED]
... Hi everyone, I'm trying to use GATK to hard filter variants but, while I'm following the GATK website's tutorial, I haven't actually been able to filter out any variants. I want to filter based on the VQSLOD flag. I tried to perform the filtering using GATK 3.8 or 4.1, but systematically, any var ...
genome gatk variantfiltration filtering snp written 13 days ago by romain.coppee0

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Scholar 12 days ago, created an answer that has been accepted. For A: GATK VariantFiltration does not filter

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