User: rse

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rse30
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New User
Location:
United States
Last seen:
5 months, 1 week ago
Joined:
3 years, 1 month ago
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Posts by rse

<prev • 40 results • page 1 of 4 • next >
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Answer: A: Loss of heterozygosity analysis from SNV files
... Thank you Yes, VarScan2 outputs LOH events from tumor-normal pair, but these are SNVs only. And since LOH is a region of allelic imbalance. How to get the region of LOH from these SNP-Indels? ...
written 5 months ago by rse30
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Comment: C: Loss Of Heterozygosity Calls On Snp Annotated File
... In order to call a region as LOH in WGS data, how many minimum homozygous SNPs should be present? ...
written 5 months ago by rse30
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Loss of heterozygosity analysis from SNV files
... Hi All, Is there any way to identify the Loss of heterozygosity region from the blood and tumor snv vcf files? Or any cut-off for minimum number of homozygous SNPs in a segment to be called a LOH? Thanks ...
next-gen sequencing written 5 months ago by rse30 • updated 8 weeks ago by Bogdan260
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Comment: C: CNV / SV Filtration
... Thank you... Yes, filtering CNVs based on SVs detected in healthy individuals based on the databases of DGV and dbVar is not correct. bUT DGV AND DBVAR have classified SVs and CNVs separately according to each type under the category - Copy loss, Copy gain, deletion, insertion, duplication, etc. So, ...
written 5 months ago by rse30
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Comment: C: CNV / SV Filtration
... Yes, it's true. Thank you :) ...
written 5 months ago by rse30
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Comment: C: CNV / SV Filtration
... Thank you. If i want to remove the variants present in healthy control population. In that case, what is the recommended cut-off ? ...
written 5 months ago by rse30
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CNV / SV Filtration
... Hi All, In case of CNV/SV filtration, what is the %age of overlap that is most widely used to filter out a CNV/SV segment after comparison with DGV and dbVar ? Also in DGV, there are few segments which has both gain and loss. So, while filtering against our CNV data, how to filter out our variants ...
genome next-gen sequencing written 5 months ago by rse30
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Answer: A: SNVer error: chrome not found in Reference
... SNVer generates a pretty big output file as compared to other variant callers. What can be the reason? Too many false positives? ...
written 13 months ago by rse30
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Answer: A: Learn to develop bioinformatics tools
... Thanks a lot for your valuable inputs. ...
written 13 months ago by rse30
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Comment: C: Learn to develop bioinformatics tools
... I know perl language, R and linux commands. ...
written 13 months ago by rse30

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