
Gökalp Çelik
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Activity overview
Latest activity by Gökalp Çelik-
Gökalp Çelik commented,
Hi Dong Wang Here is the response from the GATK-SV team. This is a known issue and it is fixed in a later version of docker image. They are recommending updating the sv_pipeline_docker variable t...
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Gökalp Çelik commented,
Hi Ramiro Barrantes The only source bam file you can get from that workflow is through STAR aligner which scores unique mapping reads with score 255 which is totally incompatible with Mutect2 and r...
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Gökalp Çelik commented,
Hi Dong Wang This could be bug at one of the tools that generate the target vcf. I will relay to GATK-SV team to check it out.
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Gökalp Çelik commented,
Hi Pranav Garg Do you get more Somatic Calls passing filter or more variant sites that indicate a contamination? According to Mutect documentation below increasing normal-lod increases the need for...
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Gökalp Çelik commented,
Hi Tanya Sarkin Jain The issue should have been resolved by now and 4.5.0.0 and onwards should be OK to use. Can you provide more details of the problem that you are facing? Can you post your logs ...
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Gökalp Çelik commented,
Hi Ramiro Barrantes What is the source of bam files you use with ASEReadCounter?
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Gökalp Çelik commented,
Hi Matteo Tommaso Ungaro There are 2 sources that you can check for our old documentation. The below article explains majority of the algorithms in concise format. https://www.nature.com/articles/...
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Gökalp Çelik commented,
Hi Leo Our recommendation is to combine different libraries of the same sample at the level of MarkDuplicates step. MarkDuplicates tool can accept more than one bam files to work with. Slight diffe...
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Gökalp Çelik commented,
Hi again. It is possible that Chr2 files or indexes could have been corrupt. Can you reindex those GVCF files and see if that works? Also CombineGVCFs may not be a very optimal solution for so many...
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Gökalp Çelik commented,
Hi Ons hamzaoui Currently there is no implementation of generating the most frequent alleles due to complexity of calculating allele frequencies of every single allele generated. As the number of a...