SkyWarrior
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Latest activity by SkyWarrior-
SkyWarrior commented,
Hi Looks like padding has provided some level of consistency for the same calls from the related members. RTN2 deletion was also called I am digging more into it.
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SkyWarrior commented,
Actually my concern was with those samples that have skewed read starts located with respect to the exon regions however with what you and Andrew said now it makes more sense since intervals are no...
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SkyWarrior commented,
I just realized after my trial that would be the way to do it. However it will certainly merge many of the short and closely packed exons into a larger interval and will reduce sensitivity when onl...
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SkyWarrior commented,
Looks like that interval was considered a common site chr19 45495095 45495139 0.511111 -2.32E-05 -10.67037244chr19 45496792 45496825 0.676471 -1.64E-06 -13.31876888chr...
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SkyWarrior commented,
Hi Andrey Smirnov Padding idea is interesting. Based on what you say it would not cause nearby intervals to be merged since padding is only applied to find the reads. Although I don't think this ma...
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SkyWarrior commented,
Same problem persists with gatk 4.1.7.0. I will try one of the earliest versions of the tool to see if it works.
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SkyWarrior commented,
Btw A few clarifications 1- Genome : hg38 from GIAB 2- İntervals are exons from the capture kit's bed file.
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SkyWarrior commented,
XHMM with a little more optimized parameters (1e-4 CNV distribution, 0.2 normalization value) captured this homozygous deletion quite nicely. I would expect simple PCA to be less precise it isn't. ...
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SkyWarrior commented,
Here is my Denoised copy ratio lines for the deleted locus chr19 45495095 45495139 1.7324975804922187chr19 45496792 45496825 0.1841071070156478chr19 45498473 45499411 1.5...
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SkyWarrior created a post,
Inconsistency between intervals.vcf and Normalized Copy ratios txt file in GCNV workflow 4.2.6.1
AnsweredHi I observed an inconsistency between these 2 files generated for 2 samples in 2 different runs of GCNV workflow using GATK 4.2.6.1 docker image. I am not sure if my problem is similar to this on...