How To Validate A Snp Calling Pipeline With A Test Bam File

Question

[win]

Hi all, I have a pipeline that and we want to make sure it works correctly. While we can test the VCF file in several ways I wanted to introduce a SNP that i know beforehand. What I mean is is it possible to change the detected sequence inside a BAM file at a certain genomic location with a new sequence that will be different from the reference sequence and should be detected in my VCF?

Any pointers will be highly appreciated.

Thanks.

Answer 1

[Pierre Lindenbaum]

a simple solution: generate your FASTQs using wgsim (it's part of the samtools package) and test if your pipeline detects the SNP generated by wgsim.

Another idea: test your tools using the VCFs and the BAMs produced by 1000KG /deep coverage: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/trio/snps/