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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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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