How to do a PCA plot on the exome data using different library kits?

Question

[mullin.yu]

Hi,

I have around 1000 exome data (fastq, bam, vcf). I want to a PCA plot on the exome data using different library kits for the QC step. I would expect the PCA plots showing clusters of samples using different library kits.

May I know any suggestion? Any software package can help? Use BAM or VCF file?

Thanks a lot!

Regards, Mullin

[ATpoint]

Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

This should give you an idea.