Question: Panel Validation using NA12878 DNA
gravatar for NielQC
23 months ago by
NielQC10 wrote:

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 HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf 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

validation giab panel na12878 ngs • 1.4k views
ADD COMMENTlink written 23 months ago by NielQC10

Hello NielQC!

It appears that your post has been cross-posted to another site:

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 10 months ago by zx87546.8k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1130 users visited in the last hour