Ahmed S. Chakroun
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Recent activity by Ahmed S. Chakroun Sort by recent activity-
Hi everyone, Please, is there any updated version available for the dbSNP_b37 later than v138. It seems like I do have the same issues because of an error in the dbsnp_138.b37.vcf.gz file. Looking ...
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Hi Benedicte N, Indeed, I confirm what Pamela said, I upgraded to the latest version and I have also updated the conda environment using the latest version .yml file. Good luck. Ahmed
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Hi Pamela, Indeed, updating the conda environment solved the issue. Now GermlineCNVCaller works fine. Thank you very much for the valuable help. Regards.Ahmed
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Hi, I am pretty sure, that's a bug with the python script being generated each time we use GermlineCNVCaller and here is the full error message I get: cohort_denoising_calling.1986139956957694084.p...
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Hi, Thanks a lot SkyWarrior. Indeed, it seems working with 4.2.3.0. However, the same command now it getting the following error: cohort_denoising_calling.16183341557554455300.py: error: unrecogniz...
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So, it's not recommended to mix exome data captured using different kits (say Agilent SureSelect V6 and V7) within the same GenomicsDB, isn't it? Thank you very much for your help.Kind regards. Ahmed
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Absolutely, I dowloaded it from the Broad Institute ftp bundle. The google bucket is exclusively for hg38.
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Hi Genevieve, Thank you very much for your reply. Please, do you have any suggestions where to find a newer version of dbSNP for build37.2? All the best. Ahmed
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Hi, I hit the same issue using VariantRecalibrator from GATK release 4.1.9.0 so I upgraded to 4.2.0.0 to check the position and it turns out that it was at position 6:29857105 with the following er...