Gökalp Çelik
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Activity overview
Latest activity by Gökalp Çelik-
Gökalp Çelik commented,
Hi Brianna Banting Your situation exactly matches to the definition of that recommended parameter. The one you used is only usable when only a single whole contig is given as interval. The recommen...
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Gökalp Çelik commented,
Hi Robert Bremel Can you check the header sections of your all BAM and VCF inputs? Something does not seem right? Regards.
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Gökalp Çelik commented,
Hi Sofya Dubovskova VariantAnnotator does not use similar ways to analyze variant sites as HaplotypeCaller so numeric values could be different between 2 tools. VariantAnnotator uses direct reads t...
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Gökalp Çelik commented,
Hi again. Mutect2 uses a completely different approach for variant filtration and joint calling using Mutect2 is not something that we published as a recommended flow. Obtained GVCF files may be c...
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Gökalp Çelik commented,
Hi caitlin newman PathSeqSpark uses built in BwaSpark tool to align reads to reference however it is not the very same version that is available as BWA (Assuming that your reads are mapped with BWA...
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Gökalp Çelik commented,
Hi huiling_mo Looks like you are trying to joint genotype mitochondria genomes however HaplotypeCaller is not the proper tool for this task. If you are interested in obtaining Allele fractions for ...
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Gökalp Çelik commented,
Hi Christina There is a way that this could happen. First you can use GATK SelectVariants tool on the GenomicsDB import that you generated and using --sample-name parameter you can specify which sa...
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Gökalp Çelik commented,
Hi again. It depends on the definition of somatic variants. HaplotypeCaller will call variants with enough QUAL and GQ values that passthrough its confidence thresholds. Some of those variants ma...
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Gökalp Çelik commented,
No it does not affect the way other ReadFilters perform. It will only disable subsampling of reads. Regards.
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Gökalp Çelik commented,
Hi Nadia If you are performing joint calling and imputation you may need to refer to the original imputation software for emitting those values since they are calculated based on the HMM performed ...