Gökalp Çelik
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Activity overview
Latest activity by Gökalp Çelik-
Gökalp Çelik commented,
Hi Shai Casif What version are you using?
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Gökalp Çelik commented,
Hi again. We do have hard filtering thresholds for human samples however you may wish to try them first to see if your calls have a solid standing for those parameters. Below is the article for exp...
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Gökalp Çelik commented,
Hi again. Sorry for our late response. What is the ploidy for your samples? Importing and Genotyping steps take more time to finish depending on the number of expected alleles per loci therefore i...
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Gökalp Çelik commented,
Hi Christopher Steel Unfortunately it is not easy for us to delineate through snakemake flows however we have a couple of suggestions to make. 1- We see that you have multiple bam inputs for Mutec...
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Gökalp Çelik commented,
Hi Robert Thomson The very first file is definitely an issue because it does not have any alternate alleles present. There is no way that tool can do anything with it since there is no alternate nu...
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Gökalp Çelik commented,
Hi Eggraandio Unfortunately, unless you have a reference variant set for your species you may have to resort to our bootstapping approach for BQSR. It involves multiple rounds of variant calling fi...
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Gökalp Çelik commented,
Hi Daniel We do have a new tool in the making named PerMutect which is a ML augmented version of Mutect2 in fact it can even be named as Mutect3 which we have pointers to its existence in the curre...
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Gökalp Çelik commented,
Hi Ramesh GCNV has 2 separate modes both of which may serve for different purposes. COHORT mode runs without a prior model and generates the model on the fly as it detects and calculates CNVs. If y...
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Gökalp Çelik commented,
Hi Rez1 Purpose of the base recalibrator is not to increase the basecalling qualities but to bring them closer to the empirical values. You may be able to check the result of recalibration using An...
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Gökalp Çelik commented,
Hi Jan Svaton Are you sure that your resource vcf is compatible with the VCF file that you are trying to annotate? Are they from the same reference genome and build? It is possible that your resou...