NGS whole genome sequence versus sequence capture for quality control

houkto · 02-02-2012, 05:16 AM

Hi there,

I am trying to compare NGS whole genome sequence data (two strains, one with x26 coverage and the other with x21 coverage) and custom agilent sequence capture of selected regions from the the above mentioned strains but with very high coverage (x10,000). Both data were analysed using the same pipeline.

Aim:
To get a percentage of how reliable my NGS data is compared to sequence capture.
and the way I am thinking of doing it is by either extract the SNPs from NGS data SNPs/indel using the targeted regions that were used in the custom sequence capture and then compared how many snps were missed by the NGS analysis. or I can pull the snps at earlier point of the analysis.

What I need to know is:
(a)What i wanted to know is what do you think of this approach, specially i have not seen it yet done by other group yet ? (if it did could you please let me know about this article).

(b) is there another way of comparing both dataset for quality control

(c) Also I wanted to know what are other possible benefits from doing such comparison ? if you think it is a good idea?

Cheers

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02-02-2012, 05:16 AM	#1
houkto Junior Member Location: UK Join Date: Sep 2011 Posts: 5	NGS whole genome sequence versus sequence capture for quality control Hi there, I am trying to compare NGS whole genome sequence data (two strains, one with x26 coverage and the other with x21 coverage) and custom agilent sequence capture of selected regions from the the above mentioned strains but with very high coverage (x10,000). Both data were analysed using the same pipeline. Aim: To get a percentage of how reliable my NGS data is compared to sequence capture. and the way I am thinking of doing it is by either extract the SNPs from NGS data SNPs/indel using the targeted regions that were used in the custom sequence capture and then compared how many snps were missed by the NGS analysis. or I can pull the snps at earlier point of the analysis. What I need to know is: (a)What i wanted to know is what do you think of this approach, specially i have not seen it yet done by other group yet ? (if it did could you please let me know about this article). (b) is there another way of comparing both dataset for quality control (c) Also I wanted to know what are other possible benefits from doing such comparison ? if you think it is a good idea? Cheers