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User: Nandini

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Nandini • 830
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830
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London
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Last seen:
2 weeks ago
Joined:
7 years, 7 months ago
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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 Nandini • 830
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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 Nandini • 830
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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 Nandini • 830
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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 Nandini • 830
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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 Nandini • 830
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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 Nandini • 830 • 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 Nandini • 830
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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 Nandini • 830
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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 Nandini • 830
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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 Nandini • 830

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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
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