User: Nandini

gravatar for Nandini
Nandini550
Reputation:
550
Status:
Trusted
Location:
London
Scholar ID:
Google Scholar Page
Last seen:
22 hours ago
Joined:
6 years, 1 month ago
Email:
n********************@gmail.com

Bioinformatician

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

Posts by Nandini

<prev • 137 results • page 1 of 14 • next >
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Comment: C: Annotation with snpEFF
... I have uploaded the file on slack ...
written 22 hours ago by Nandini550
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Comment: C: Annotation with snpEFF
... Should I paste it here or upload it on slack as DM ? Its a file with ~20 variants ...
written 1 day ago by Nandini550
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Comment: C: Annotation with snpEFF
... My question is 1) Is there a way to avoid non-ref seq annotations such as `4PED:A_480-A_522` `4IDN:B_77-B_117` 4PED:A_480-A_522:NM_020247.4,4PED:A_480-A_523:NM_020247.4,4PED:A_480-A_636:NM_020247.4,4PED:A_480-A_640:NM_020247.4,4PED:A_480-A_643:NM_020247.4,NM_020247.4 4IDN:B_77-B_117: ...
written 1 day ago by Nandini550
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Comment: C: Annotation with snpEFF
... yup, unfortunately, we need to report all transcripts as we are working under a clinical setting. ...
written 1 day ago by Nandini550
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Comment: C: Annotation with snpEFF
... Hi fin swimmer, So if you see the result snippet in the last column, the HGVS_P columns, when extracted looks like this ANN[*].HGVS_P** .,.,.,.,.,p.Phe480Phe .,.,.,p.Glu117Glu,p.Glu117Glu,p.Glu117Glu .,.,.,.,.,. .,.,. ...
written 1 day ago by Nandini550
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Annotation with snpEFF
... I have been using the following commands to annotate my vcf file with Refseq annotation on SnpEff 4.3t, followed by snpsift to extract columns of interest. java -Xmx4g -jar snpEff.jar hg19 $panel.sorted.vcf > $panel.snpeff.hg19.vcf java -jar SnpSift.jar extractFields -s "," -e "." $pane ...
vcf annotation extractfields snpeff written 1 day ago by Nandini550
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Answer: A: How to filter variant calls based on specific reference and alternate allele fre
... You can use GATK's [SelectVariants][1] to filter variants of interest based in several criteria [1]: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php ...
written 1 day ago by Nandini550
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Answer: A: How to get SNP annotation with 3-letter amino acid abbreviation?
... [Variant Effect Predictor][1] should be able to give you the 3-letter amino acid abbv as the output. [1]: https://www.ensembl.org/info/docs/tools/vep/index.html ...
written 4 weeks ago by Nandini550
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CNV calling using ExomeDepth
... Hello, I'm working to establish a pipeline for germline CNV calling. Our target consists of 150 genes with approx 1500 exons. Out data is HiSeq data (96 samples per run) To establish a good reference set, I'm following [this paper][1] to calculate the inter-sample variation in coverage, using the ...
exomedepth reference cnv written 5 weeks ago by Nandini550 • updated 5 weeks ago by andrew.j.skelton735.0k
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Comment: C: mm10: Sequence length difference between interval file and reference
... Yes its mm10. This interval file is being prepared to be used for GATK variant calling. ...
written 3 months ago by Nandini550

Latest awards to Nandini

Popular Question 7 weeks ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For extract SNPs from compressed PLINK files
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Great Question 3 months ago, created a question with more than 5,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Appreciated 3 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 3 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 3 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 3 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 5 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Scholar 5 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 6 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Centurion 6 months ago, created 100 posts.
Popular Question 6 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 8 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 How to interpret heterozygosity rate ?
Popular Question 16 months ago, created a question with more than 1,000 views. For Convert .Pre Files To .Ped And .Map Files For Plink
Popular Question 18 months ago, created a question with more than 1,000 views. For Low Coverage Depth On Exome Sequencing
Great Question 24 months ago, created a question with more than 5,000 views. For Whole Genome Analysis Pipeline (Illumina)
Great Question 24 months ago, created a question with more than 5,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Low Coverage Depth On Exome Sequencing
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Low Coverage Depth On Exome Sequencing
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Low Coverage Depth On Exome Sequencing
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Whole Genome Analysis Pipeline (Illumina)
Appreciated 2.7 years 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
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Rare Variant Snps With No Allele Frequency

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