
Khalil Jahed
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Activity overview
Latest activity by Khalil Jahed-
Khalil Jahed commented,
Hi Genevieve Brandt (she/her), Comparing the quality score accuracy of before and after ApplyBQSR, the accuracy has been improved afterward where the mean quality score decreased - which I think is...
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Khalil Jahed created a post,
ApplyBQSR reduces reads quality
ApplyBQSR reduced reads quality from 70 to 50 (in ASCII scale). The known-sites used in this step, were first generated from the same sample without ApplyBQSR. These variants were limited to only h...
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Khalil Jahed commented,
Similar question I have. How can one find these known sites for non-model organisms eg. crops?
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Khalil Jahed created a post,
Variant Filtration - FS and SOR are not supported
AnsweredHi, The FS and SOR variant filtration options do not work. Are they still active? NOTE: AB and MQ work using the same command. GATK/4.14.1 was used. Command lines: gatk VariantFiltration \ -R ref...
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Khalil Jahed commented,
Hi Sushma, I got updated!
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Khalil Jahed created a post,
Where to find old discussion
Hi, It seems that the old discussion on this forum is not accessible. Can we still retrieve those posts and comments?