User: Nandini
Nandini • 550
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Bioinformatician
Develop pipeline(s) for WES, Targeted gene sequencing, mtDNA NGS analysis
Posts by Nandini
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C: Annotation with snpEFF
... I have uploaded the file on slack ...
written 22 hours ago by
Nandini • 550
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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
Nandini • 550
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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
Nandini • 550
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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
Nandini • 550
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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
Nandini • 550
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... 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 ...
written 1 day ago by
Nandini • 550
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... 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
Nandini • 550
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... [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
Nandini • 550
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... 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 ...
written 5 weeks ago by
Nandini • 550
• updated
5 weeks ago by
andrew.j.skelton73 ♦ 5.0k
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... Yes its mm10.
This interval file is being prepared to be used for GATK variant calling. ...
written 3 months ago by
Nandini • 550
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For Pros and cons of Illumina HiSeq and Next Seq
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For Low Coverage Depth On Exome Sequencing
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For Low Coverage Depth On Exome Sequencing
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