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Old 05-05-2017, 03:36 AM   #1
NielQC
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Location: Valencia

Join Date: Nov 2016
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Default Panel Validation using NA12878 DNA

Hi there,

we have made a panel that comprises several (190) exonic alterations and now we want to test how capable are we to call these variants starting from a DNA sample. This post is for retrieve suggestions about how can we do this and/or to know if my approach is not correct.

Basically what I have been thinking about is purchasing NA12878 DNA from Coriell Institute, sequencing it and running a variant calling pipeline (without going into details, mapping vs GRCh37 and call variants with mpileup). Once I have the variants, check them vs the high-confidence calls set focusing on my 190 exonic alterations and if the alleles matches at these positions would mean that we call these variants correctly.

Is this a correct way?

Previously, aiming to evaluate just the bioinformatic pipeline and not the laboratory part, I did the same analysis with the GIAB NA12878 dataset (HiSeq x300) and checked the output variants with this callset ftp://ftp.ncbi.nlm.nih.gov/giab/ftp/...ransfer.vcf.gz available at the GIAB ftp site. Previously I normalized the variants representation of both calls sets using *vcflib vcfallelicprimitives*.

And a last question. For my validation purpose, is there any difference between purchasing the NIST reference DNA and purchasing the Coriell Institute DNA Sample? I think it's the same, but look the difference in prices...

Any suggestion will be welcome

Last edited by NielQC; 05-05-2017 at 04:00 AM.
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