ulitskyi
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Activity overview
Latest activity by ulitskyi-
ulitskyi commented,
Hi Genevieve, I've uploaded a detailed bug report with three other cases of the same problem (along with the bam slices and the commands, all in problems_ulitskyi.zip). All of these are obvious cal...
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ulitskyi commented,
Dear Genevieve, Thank you for checking. We indeed use "--max-reads-per-alignment-start 0", but that does not help with the occasional miscalls mentioned in this thread. I'm referring to very clear ...
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ulitskyi commented,
Thank you Genevieve. I can post the example there. Note that downsampling is not really a solution that seems to work consistently well, as some regions behave better with downsampling while others...
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ulitskyi commented,
Hi Genevieve, Yes, I uploaded the data upfront. We don't use NotDuplicateReadFilter, since the data is for targeted multiplex amplicon sequencing. We experimented a lot with different max-reads-per...
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ulitskyi commented,
Hi, any news on this issue? Thanks, Igor.
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ulitskyi created a post,
HaplotypeCaller fails at regions of high depth
I'm looking a region from a targeted sequecing run. It is sequenced at high depth (~60K). If only 10,000 or even 40,000 reads per alignment start are used, there is no problem, and the region is ca...