User: Gennady Khvorykh

Reputation:
90
Status:
Trusted
Location:
Russia/Moscow/Institute of Molecular Genetics of the Russian Academy of Sciences
Website:
http://inzilico.com/
Last seen:
3 months ago
Joined:
2 years, 1 month ago
Email:
g***************@gmail.com

Posts by Gennady Khvorykh

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Calculating frequencies of possible combinations of SNP genotypes in a populatio
... I would formalize the task like this. We need to calculate the probability of three independent events happened together. The event is the choice of the genotype at the locus (SNP). The probability is estimated by the genotype frequency. Assuming the Hardy-Weinberg equilibrium is true, the frequency ...
written 5 months ago by Gennady Khvorykh90
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Comment: C: BGIseq 500 - raw data files
... Thank you for the comment. I'm curious about raw data that precede the fastq files. In the case of Illumina, these are bcl files. They represent the intensities which are further converted to sequences given as fastq files. The conversion is made automatically but sometimes there is a need to do it ...
written 8 months ago by Gennady Khvorykh90
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BGIseq 500 - raw data files
... Does BGIseq 500 produce raw data files similar to Illumina's bcl ones? What extension do they have? Which folder does it write them? Your experience are quite appreciated. ...
bcl bgi written 8 months ago by Gennady Khvorykh90
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Comment: C: How to calculate Imputation Accuracy Estimates like concordance with BEAGLE?
... To estimate the quality of imputation, I think, imputed.vcf should be compared with all.vcf.gz and not with eval.vcf.gz :) ...
written 12 months ago by Gennady Khvorykh90
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Answer: A: Strand Alignment in ShapeIt -- "Reference and Main panels are not well aligned"
... I had a data set with unknown human genome assembly. I figure out it by intersecting the positions taken from dbSNP130 (hg18) and dbSNP150 (hg19). With incorrect assembly only 0.9% of positions were in common. According to SHAPEIT -check, you have 0.9% of SNPs in reference. Why not to double check t ...
written 13 months ago by Gennady Khvorykh90
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Answer: A: Convert numeric alleles into letters
... Cause legend$a0 and legend$a1 are factors. Convert them into character class. require(data.table) # Initilize data1 <- " rsID position_b36 a0 a1 rs7575818 134788398 A G rs3791281 134792091 A G rs876887 134793655 G A rs4953912 1347 ...
written 16 months ago by Gennady Khvorykh90
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Answer: A: Convert numeric alleles into letters
... *sorted* has class `data.frame`. The [above code][1] I used to convert numerical haplotypes into lateral ones works if this variable has class `data.table`. Not all `data.table` syntax can be applied for `data.frame`. Possible quick fix: library(data.table) # Convert data.frame into da ...
written 16 months ago by Gennady Khvorykh90
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Comment: C: Convert numeric alleles into letters
... Could you provide a reproducible code? It should reflect how *sorted* and *legend* variable were defined. Paste also examples of data sets loaded into *sorted* and *legend*. ...
written 16 months ago by Gennady Khvorykh90
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Answer: A: Need earlier version of fastPHASE
... It looks like input file `plink2fastphase_chr1.recode.phase.inp` wasn't parsed by the script. Could you send me the file or 10 first rows of it? I'll tune the code. Send all information to info [at] inzilico.com. ...
written 17 months ago by Gennady Khvorykh90
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Answer: A: Fastphase cluster determination
... Here [a workflow][1] I created to estimate K in fastPHASE. Everybody is welcome to explore it. [1]: https://github.com/inzilico/kselection ...
written 18 months ago by Gennady Khvorykh90

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Popular Question 4 months ago, created a question with more than 1,000 views. For Convert numeric alleles into letters

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