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The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence...
Background Minor allele detection in very high coverage sequence data (>1000X) has many applications such as detecting mtDNA heteroplasmy, somatic mutations in cancer or tumors, SNP calling in pool sequencing, etc., where reads with low frequency are not necessarily sequence error but may instead convey biological information. However, the suitability of common base quality recalibration tools...
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