High-throughput sequence variant analysis: Using BAM or VCF files?

Question

[Zahra]

Hi all,

I want to analyze the variation status of some genes in some cancer, And for this purpose want to use the ICGC data (there is a large number of patients). Now I have two choices :

1. Downloading the VCF files of patients and analyze them.
2. Downloading the BAM file of my interest gene position and create the VCF file, then analyze them.

According to my purpose, which option is more recommended and accepted?

Thanks for any help

Answer 1

[ATpoint]

VCF contains variant calls. If you want to use the results they produced then use VCF. BAM contains aligned reads. That would require variant calling yourself and then analyse the resulting VCF. You probably want to simply use their VCFs for exploratory analysis as everything else requires quite some computation first.