User: Nandini

gravatar for Nandini
Nandini810
Reputation:
810
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Trusted
Location:
London
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Last seen:
5 days, 4 hours ago
Joined:
7 years, 1 month ago
Email:
n********************@gmail.com

Bioinformatician

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

Posts by Nandini

<prev • 201 results • page 1 of 21 • next >
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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 weeks ago by Nandini810
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Comment: C: Identify or update refseq transcript version on snpeff
... No, we haven't as yet. ...
written 7 weeks ago by Nandini810
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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 12 weeks ago by Nandini810
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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 12 weeks ago by Nandini810
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... It will be good if you are able to paste all your commands as we can see the parameters used. what are the commands for Varscan ? ...
written 12 weeks ago by Nandini810
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Comment: C: Downsample BAM for targeted NGS panels
... So why did you use a random seed of 50 here ? ...
written 3 months ago by Nandini810
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Comment: C: Downsample BAM for targeted NGS panels
... That's pretty much the plan - to downsample from 50% to 10% and then check for its read depth. I was opting for my second option of doing it just once but I was suggested to downsample the same BAM thrice and then take its average read depth ...
written 3 months ago by Nandini810
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Comment: C: Downsample BAM for targeted NGS panels
... ive edited a bit of my question - so does this help with the reproducibility as well ? ...
written 3 months ago by Nandini810
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Downsample BAM for targeted NGS panels
... Hello I am downsampling BAMs down to 10% on control samples to check at what minimum read depth are we able to detect a certain set of SNPs. What approach do people usually adopt for this 1) downsample the same BAM 3 times with different seed options and then take the average of the read dept ...
targeted-ngs downsample sambamba written 3 months ago by Nandini810 • updated 7 weeks ago by shrirambhosle30
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Comment: C: how to convert a list of genes to BED file?
... Have you tried [UCSC table browser][1] ? [1]: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=711027113_pLhHGH6YmOysUzCgwrfAnskhsBBg ...
written 4 months ago by Nandini810

Latest awards to Nandini

Popular Question 3 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 6 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Single rare variant approaches
Popular Question 7 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Great Question 8 months ago, created a question with more than 5,000 views. For How to interpret heterozygosity rate ?
Great Question 8 months ago, created a question with more than 5,000 views. For Calculate z-scores from GWAS summary stats
Popular Question 9 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
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Epic Question 11 months ago, created a question with more than 10,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Popular Question 13 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 13 months ago, created a question with more than 1,000 views. For extract SNPs from compressed PLINK files
Popular Question 14 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Great Question 15 months ago, created a question with more than 5,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Appreciated 15 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
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How To Revert Allele Data To Atgc With Plink After Recoding To 12 Format
Scholar 15 months ago, created an answer that has been accepted. For A: where to get the gene annotations for the latest build 37 - for plotting regiona
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How To Revert Allele Data To Atgc With Plink After Recoding To 12 Format
Popular Question 17 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Scholar 17 months ago, created an answer that has been accepted. For A: where to get the gene annotations for the latest build 37 - for plotting regiona
Popular Question 18 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
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Popular Question 18 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
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Popular Question 2.4 years ago, created a question with more than 1,000 views. For Convert .Pre Files To .Ped And .Map Files For Plink

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