Remapping of high coverage WGS reads of the 1000 Genomes Project to GRCh38

The high coverage PCR-free WGS sequencing reads for 24 samples of the 1000 Genomes Project were aligned to GRCh38. In this study, ALT-aware BWA-mem developed by Heng Li (https://github.com/lh3/bwa/blob/master/README-alt.md) was used to map the 1000 Genomes Project reads to GRCh38. The initial BAMs were fine-tuned by realigning around indels, removing duplicates and recalibrating quality scores. At the end, the BAM files were further compressed to CRAMs. The whole process was managed by Ensemble HIVE system in a parallel fashion on computer farm.