R04 Errata

The following issues have been identified subsequent to release R04; they will be addressed in an upcoming release:

  • The VEP-annotated VCFs from the GREGoR joint callset contain incorrect VRS identifiers. These remain correct in the corresponding unannotated VCFs.
  • The files associated with aligned_pac_bio_ids GSS228799-01-011-LG-2 and GSS128794-01-010-LG-2 are unintended duplicates and should not be used.
  • The following files are duplicates of other bams and may be deleted in the future:
    • gs://fc-secure-a1f0d27d-c9d5-48bc-b4ba-5e0f81784fb1/GSS179904/SR_GS/GSS179904-3147-4e0bd01a-6bf2-4731-a054-0f8685bd8d62_reheadered.bam
    • gs://fc-secure-a1f0d27d-c9d5-48bc-b4ba-5e0f81784fb1/GSS179907/SR_GS/GSS179907-3148-05e96cd4-84d9-4274-a05f-cc9240b2f7ef_reheadered.bam
    • gs://fc-secure-a1f0d27d-c9d5-48bc-b4ba-5e0f81784fb1/GSS279909/SR_GS/GSS279909-3146-fc594df4-589c-446a-a6e3-f3af55ad237b_reheadered.bam
    • gs://fc-secure-ab18917b-873b-4082-8181-7653393999c9/GSS293189/LR_GS/pacbio/GSS293189_r64282e_20230419_021750.GCA_000001405_15.haplotagged.bam
  • PMGRC-1076-1065-3 and PMGRC-1079-1065-3 have been identified as swapped in the short read WGS data.
  • PMGRC-423-423-0 and PMGRC-425-423-1 have been identified as swapped in the PacBio data.
  • The following participants' PacBio data have been flagged for excess human source contamination: PMGRC-2109-2109-0, PMGRC-380-381-1, PMGRC-82-82-0
  • The PacBio data for PMGRC-418-418-0 has metadata discrepancies.
  • PMGRC-478-478-0 and PMGRC-479-478-2 have been identified as swapped in the short read RNA-seq data.
  • The RNA-seq data for PMGRC-838-839-2 have been flagged as potentially contaminated.
  • The short read RNA-seq data for PMGRC-104-104-0, PMGRC-1116-1116-0, and PMGRC-1229-1229-0 have metadata discrepancies.
  • The following short read RNA-seq data are flagged for QC failures (low RIN, insufficient percent human reads, insert size distribution, GC content, percent duplication): PMGRC-45-43-1, PMGRC-1203-1200-1, PMGRC-1076-1065-3, PMGRC-88-88-0, PMGRC-125-125-0, PMGRC-924-924-0, PMGRC-1065-1065-0, PMGRC-265-265-0.