Capture-enriched non-recombining Y-chromosome sequencing data from southwestern Angola

We generated non-recombining Y chromosome (NRY) sequence data from 170 individuals with previously reported mitochondrial genomes (mtDNA), to investigate the population history of diverse southwestern Angolan groups and to study the causes and consequences of sex-biased processes in their genetic variation. Double-indexed libraries were capture-enriched for 2.3 Mb of the target NRY. Paired-end sequencing data were generated on the Illumina HiSeq 2500 platform and standard Illumina base-calling was performed using Bustard. We trimmed Illumina adapters and merged completely overlapping paired sequences using leeHOM, and de-multiplexed the pooled sequencing data using deML. The sequencing data were aligned to the human reference genome hg19_1000g using BWA (v0.5.10) aln algorithm with default parameters. This release contains the subset of reads that aligned to the 2.3Mb Y-chromosome region targeted by capture-enrichment.