User: Shab86

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Shab86220
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Helsinki
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Posts by Shab86

<prev • 38 results • page 1 of 4 • next >
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Comment: C: imputation and changing genotypes in Beagle and FImpute
... I know it doesn't but I want to use duoHMM first and then use FImpute vs FImpute alone to check whether any mendel errors are prevented or not and if yes, then by how much. Beagle though quite fast won't give you genotype changed information. ...
written 10 months ago by Shab86220
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Answer: A: imputation and changing genotypes in Beagle and FImpute
... If you want to utilize pedigree information for imputation later on, why not use the SHAPEIT's duoHMM tool for better pre-phasing of your genotyped datasets. Then you could go for imputation using either FImpute or Beagle. Doing this would reduce computational costs and errors too. ...
written 10 months ago by Shab86220
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Comment: C: installing usearch on Mac
... @genomax is quite correct here. Edit your post with the exact errors you get while installing/running it. ...
written 10 months ago by Shab86220
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Answer: A: VCF to BED conversion error in BEDOPS
... So, probably this and incomplete .bed output are because of the sorting step which might cause the `/tempdir` to be filled up. A workaround for this, this to use this in addition to my above commands: `--do-not-sort`. For now, it's working! ...
written 10 months ago by Shab86220
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VCF to BED conversion error in BEDOPS
... I have been using the latest version of convert2bed (from bedops) to convert VCF format to BED. But have been getting this error: convert2bed -i vcf /files/stuff.bed BED row length exceeds capacity at line 1 in -. Check that you have unix newlines (cat -A) or increase TOKENS_MAX_LENGT ...
vcf bed bedops written 10 months ago by Shab86220 • updated 10 months ago by Alex Reynolds26k
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Comment: C: How to estimate the minimal amount of sequencing required for a biomarker analys
... Are you going to conduct RNA-seq on those two intervals? Or is it some targeted sequencing that you are looking for? ...
written 10 months ago by Shab86220
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Recombination rates for phasing & imputation
... I am using LDHAT to calculate a population-specific recombination map. The output from LDHAT gives rho values (population recombination rate) on a per-position basis. However, to use this genetic map for phasing or imputation, I need the values in cM/Mb. For example, the genetic map used in phasing: ...
ldhat recombination genomics written 10 months ago by Shab86220
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How to convert recombination rate data from LDHAT into a recombination map for imputation in IMPUTE2
... I have been using LDHAT to get recombination maps for a dataset I am currently working on. I get the output quite fine i.e., all the positions and their respective mean/median rho with 95% CI : [LDHAT Output, first column position in kb and second column is rho][1] However, when using this map wi ...
recombination ld genetic map written 10 months ago by Shab86220
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Comment: C: How to convert vcf to 23andme format
... Ahh, my mistake in interpreting it the other way around. Have you tried this: https://github.com/2sh/vcf-to-23andme ...
written 12 months ago by Shab86220
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Answer: A: How to convert vcf to 23andme format
... There are a couple of ways to convert 23andme dataset to vcf: 1. Download 23andme dataset as a tab-delimited file with just these columns: the marker ID, chromosome name, position, and the genotype. Then use bcftools to convert the tsv file above to vcf by this: `bcftools convert --tsv2vcf input.g ...
written 12 months ago by Shab86220

Latest awards to Shab86

Popular Question 10 months ago, created a question with more than 1,000 views. For Error while running BEAGLE for genotype imputation
Popular Question 10 months ago, created a question with more than 1,000 views. For How to calculate Imputation Accuracy Estimates like concordance with BEAGLE?
Popular Question 10 months ago, created a question with more than 1,000 views. For Convert Expression Set into a Matrix or Data Frame
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: statistical analysis of RNA-seq data
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: statistical analysis of RNA-seq data
Voter 2.2 years ago, voted more than 100 times.
Scholar 2.4 years ago, created an answer that has been accepted. For A: difficulty in underestanding terms and graphs
Supporter 2.4 years ago, voted at least 25 times.

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