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- Daniele Capocefalo (wariobrega)
Hi Sheila, Thanks again for your interest in this concern. It may be that the extremely larger size of dbSNP150 compared to dbSNP138 may cause the issue. On the other hand, this missing annotation occurred once every 10k variants, so the problem ca…
Hi Sheila, Thanks for your reply. I uploaded the reference genome I used (a cleaned version of hg19 downloaded from UCSC) to the ftp server in a tar.gz file named wariobrega_GATK_Debug_missingrsIDs_ReferenceGenome.tar.gz. There you'll find both th…
HI Sheila, I've uploaded a case through your FTP as you requested. The file containing a case of missing rsIDs is in a .tar.gz file named wariobrega_GATK_Debug_missingrsIDs.tar.gz. In It you'll find * The command I used in a .sh script; * the 2 GAT…
Hi Sheila, I'll send a bug report, thanks for your attention!
@Sheila Thanks a lot for your quick reply! now it's much more clearer :D I'll dig into the articles as well ASAP! Thanks again, Daniele
(Quote) Also, another thing that is now coming up to my mind: you stated that the AD consider the UNFILTERED allele depth, however, its sum is inferior to the DP, which you state being filtered. How is that possible?
Hi Sheila, and thanks for the quick reply! Your answer clarifies me a lot of doubts I was having! However, I still don't understand why the bam generated with the --bamOutput option in Haplotype Caller should contain these reads that are filtered b…