Combine single sample vcfs together

Question

[sumudu_rangika]

Hi,

I have 8 bam files ( obtained from 8 isolates from same species) and need to call variants. In order to get a final more confident SNP set I have decided to call variants using 5 different SNP callers and finally to get their intersect and filter appropriately.

One such tool I selected is Samtools mpileup. Although this tool is capable of multi-sample SNP calling, due to my limited memory capacity I'm unable to run them all together. My question is, If I call SNPs independently for each sample and later combine the 8 vcfs using (e.g. vcf-merge) would this course any issue in downstream analysis?

Appreciate your advices.

Best Regards Rangi

Answer 1

[Ron]

See this post:

http://gatkforums.broadinstitute.org/gatk/discussion/53/combining-variants-from-different-files-into-one

From the post :

"The third case is when you want to combine variant calls that were produced from the same samples but using different methods, for comparison. For example, if you're evaluating variant calls produced by different variant callers, different workflows, or the same but using different parameters. This produces separate callsets for the same samples, which are then easier to compare if you combine them into a single file. For that purpose, you can use CombineVariants, which is capable of merging VCF records intelligently, treating the same samples as separate or not as desired, combining annotations as appropriate. This is the case that requires the most preparation and forethought because there are many options that may be used to adapt the behavior of the tool.""

[sumudu_rangika]

Thanks Ron. Your answer helped me to figure out things.....