
ulitskyi
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Latest activity by ulitskyi-
ulitskyi created a post,
Spurios indel
REQUIRED for all errors and issues: a) GATK version used: 4.3.0b) Exact command used: java -Xmx6g -jar gatk-package-4.3.0.0-local.jar HaplotypeCaller -R hg19.fa -L dummy.bed -mbq 15 -G StandardA...
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ulitskyi commented,
Thanks James. We've actually tried all of these varying parameter changes, and yet as Eve indicates as well, none of them solve the problem, as at some number of reads (which varies by region/sampl...
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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...