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What is a parsimonious way to determine if two bam files are from the same individual? Is there an off-the shelf, open source implementation?
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I'd just run them through the same genotyper and then compare the genotypes with vcf-compare in vcf-tools. Or run it through a somatic detection program like VarScan2, and expect to see very few differences output. -
I've done this before with array data as validation for SNPs; when looking at SNP calls on the array spots, I would always get well over 90% concordance between calls if the same person was sequenced in multiple libraries. Between different people I would never get over 50% concordance, and this is just looking at relatively common SNPs on the array. So if you call SNPs and look at ones with at least a quality score of say 30 and coverage of 10x (by mpileup), it should be super obvious.Comment
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