Which reference genome is being used to align the reads?

We have hg19 and hg38.

We removed the following haplotypes from hg19:

  • chr4_ctg9_hap1
  • chr6_apd_hap1
  • chr6_cox_hap2
  • chr6_dbb_hap3
  • chr6_mann_hap4
  • chr6_mcf_hap5
  • chr6_qbl_hap6
  • chr6_ssto_hap7
  • chr17_ctg5_hap1