Originally posted by mrfox
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Alternatively, CNVkit works more like your proposal, where a reference copy number profile is initially constructed from a pool of normal BAM files and then reused to infer CNVs in individual samples. CNVkit can also operate without any normal-sample reference at all, but results will be slightly noisier.
Originally posted by mrfox
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Most program for copy number inference will give you some indication of how the reference should be built and whether you should process one sample at a time or the whole cohort at once.
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