User: Nandini
Nandini • 660
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Bioinformatician
Develop and maintain pipeline(s) for WES, Targeted gene sequencing, mtDNA NGS analysis
Posts by Nandini
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C: CNV and pseudogenes
... of course, we MLPA everything before reporting but also trying to build a reliable bioinformatics pipeline ...
written 2 hours ago by
Nandini • 660
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C: CNV and pseudogenes
... True, I agree but we are more in a clinical setting than research so its generating data per panels.. i guess it's just finding an appropriate way of deal with this in a diagnostic environment ...
written 2 hours ago by
Nandini • 660
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... Hello,
I'm using ExomeDepth to detect CNVs and I'm providing a bed file for all our targeted gene panels.
We know there is a processed pseudogene in a region, am just wondering if this would confound CNV calling in other genes? If it knocks off the ‘average’ coverage ?
Is it worth excluding su ...
written 6 hours ago by
Nandini • 660
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C: Tools to detect CNV for NGS-mtDNA
... okay, i'll try out a couple of CNV callers. ...
written 8 days ago by
Nandini • 660
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C: Tools to detect CNV for NGS-mtDNA
... yes, its only the mtDNA that has been sequenced entirely .
Does Lumpy include the breakpoints info for each CNV detected ? ...
written 8 days ago by
Nandini • 660
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... Hello,
Wondering if there are tools to detect CNV (duplications and deletions) for mitochondrial NGS analysis (clinical setting) ?
Not sure if I can use ExomeDepth for the same ?
Thank you ...
written 8 days ago by
Nandini • 660
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... Hi MatthewP,
So I use varscan `mpileup2SNP` and `mpileup2indel` and then combine the two result files, followed by annotation.
If you are using GATK, then I THINK you can use GATK's Mutect rather than Haplotypecaller (though I do not have much experience with GATK and mtDNA analysis) ...
written 16 days ago by
Nandini • 660
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... if it says `95` then its quite low. Its under clustered ...
written 26 days ago by
Nandini • 660
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... Thanks Both. Another quick question, is there a way to select the seed or is it totally random ? ...
written 26 days ago by
Nandini • 660
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... so does this means "S" sets the seed of 0 and only 10% of the reads by samtool ? I was going to to use sambamba for downsampling but I guess they are both similar - PE mates are lost, I think on downsampling ...
written 26 days ago by
Nandini • 660
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