Ahmed S. Chakroun
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Activity overview
Latest activity by Ahmed S. Chakroun-
Ahmed S. Chakroun commented,
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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Ahmed S. Chakroun created a post,
MergeBamAlignment for mitochondrial variant discovery
AnsweredHi, I am getting stuck in the MergeBamAlignment step of the Mitochondrial short variant discovery best practices workflow. In fact, I am working with the build37.2 reference and to run MergeBamAlig...
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Ahmed S. Chakroun commented,
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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Ahmed S. Chakroun commented,
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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Ahmed S. Chakroun commented,
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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Ahmed S. Chakroun commented,
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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Ahmed S. Chakroun created a post,
GermlineCNVCaller prefix string too short
Hi everybody, Unfortunately, I am getting stuck because the filename length of my hd5 is too short (< 3) to be used as prefix by the GermlineCNVCaller. So, I am posting just to check that nothing i...
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Ahmed S. Chakroun commented,
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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Ahmed S. Chakroun commented,
Absolutely, I dowloaded it from the Broad Institute ftp bundle. The google bucket is exclusively for hg38.
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Ahmed S. Chakroun commented,
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