check whether two bam files are sequenced from the same sample

Question

[Ming Tommy Tang]

Hi,

I have paired ChIP-seq (36bp single-end) and WES (100 bp paired-end) data from the same sample, I want to make sure the samples are not mixed up. So, I want to check whether the ChIP-seq bam and WES bam are from the same sample.

I think I can run a genotyper (freebayes, GATK unifiedGenotyper etc...) on those bam files and compare the common SNPs, but I want to know if there are any existing tools for the same task. I just saw bam-matcher https://bitbucket.org/sacgf/bam-matcher

Because I am comparing bam files from different assays, what caveats should I be aware of?

Thanks a lot!

Ming

[trausch]

Indeed, to detect sample swaps we usually re-genotype common 1000 Genomes SNPs in both samples and then do a scatter plot of the variant allele frequencies (or B-Allele Frequencies) + the correlation coefficient. This works well for WES and WGS but one caveat for ChIP-Seq is allele-specific binding. If you sill have some input material left you may just want to do DNA fingerprinting on both samples which requires only a few nanograms of DNA.

[Ming Tommy Tang]

Thanks for your suggestions. I will come back to report when I have it done.