User: Nandini

gravatar for Nandini
Nandini830
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830
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Trusted
Location:
London
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Google Scholar Page
Last seen:
2 weeks ago
Joined:
7 years, 7 months ago
Email:
n********************@gmail.com

Bioinformatician

Develop and maintain pipeline(s) for WES, Targeted gene sequencing, mtDNA NGS analysis

Posts by Nandini

<prev • 207 results • page 1 of 21 • next >
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Comment: C: If the odds ratio of a SNP is < 1, does that mean the minor allele is protective
... I know this is irrelevant now but being a part of this project, I feel the need to mention that we did correct for covariates such as age, sex and principal components to adjust for possible population stratification. It is also mentioned in the methods section of the paper ...
written 3 months ago by Nandini830
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Comment: C: Convert vcf phased data to plink
... Ah, for now, I was able to sort my issue out using the R package SNPrelate. It takes in the vcf file as input, calculates IBS and then if one feels like it, it can also convert it to PLINK format ! ...
written 4 months ago by Nandini830
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Comment: C: Convert vcf phased data to plink
... still the same. I don't think PLINK can handle phased Haplotype file in the format 0|1, where 0 indicates ref and 1 is for the alt allele. Can it ? ...
written 4 months ago by Nandini830
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Comment: C: Convert vcf phased data to plink
... No, so this is what I did (playing around with a chunk of chr22) ##convert vcf to plink ./plink --vcf input_genotype.vcf --keep-allele-order --allow-extra-chr 0 --make-bed --out MyData ##tried to calculate IBS using King /king -b MyData.bed --ibs The result from above is an ...
written 4 months ago by Nandini830
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Comment: C: Convert vcf phased data to plink
... thanks Kevin, I try to do that but end up wit a file that has 0 for each individual. ...
written 4 months ago by Nandini830
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Convert vcf phased data to plink
... I have a phased haplotype format vcf file that looks like this ##fileformat=VCFv4.0 ##reference=human_b36_both.fasta ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 NA12892 NA12878 NA19239 NA19238 NA19240 22 47812545 rs576981 ...
vcf phased-haplotype plink convert written 4 months ago by Nandini830 • updated 4 months ago by Gabriel R.2.6k
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Answer: C: hg19 interval list
... maybe not on the gatk bundle site. But probably a [liftover][1] should work ? [1]: https://genome.ucsc.edu/cgi-bin/hgLiftOver ...
written 6 months ago by Nandini830
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Comment: C: Identify or update refseq transcript version on snpeff
... No, we haven't as yet. ...
written 7 months ago by Nandini830
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... So is it WGS or WES or targeted ? ...
written 8 months ago by Nandini830
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Answer: A: How can I convert .ped file to bed+bim+fam file using plink 1.9?
... Have you read the manual ? The error you get "--file expects a filename prefix; '.ped' and '.map' are automatically appended." is self explanatory. Please remove the prefix '.ped' The command should be plink --file 50_samples --make-bed --out 50_samples_try ...
written 8 months ago by Nandini830

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Error in Snp set analysis using MetaSKAT
Popular Question 10 weeks ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 3 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
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Popular Question 5 months ago, created a question with more than 1,000 views. For Error in Snp set analysis using MetaSKAT
Great Question 5 months ago, created a question with more than 5,000 views. For How to interpret heterozygosity rate ?
Popular Question 9 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Single rare variant approaches
Popular Question 11 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 12 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
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Great Question 13 months ago, created a question with more than 5,000 views. For Calculate z-scores from GWAS summary stats
Popular Question 14 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Epic Question 16 months ago, created a question with more than 10,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Popular Question 18 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 18 months ago, created a question with more than 1,000 views. For extract SNPs from compressed PLINK files
Popular Question 19 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Great Question 20 months ago, created a question with more than 5,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Appreciated 20 months ago, created a post with more than 5 votes. For A: How To Revert Allele Data To Atgc With Plink After Recoding To 12 Format
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Popular Question 22 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?

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