We thank the authors for their diligent responses to our queries and revision proposals for the
latest draft of the paper.

We find that the addition of figure 4 to describe the extraction of haplotypes adds a lot of value
to the paper and increases the chances of data reuse. The supplementary table 5 along with the
updated wording about genomic libraries vs participants will be very helpful for readers to
understand the data contents.

We note that at the time of review:

- The dbGaP record accession number mentioned in the paper (phs000905.v1.p1) does not exist
yet.
- We have no access to the updated location of files on the GigaDB server to check that all the
files mentioned in the paper are indeed available. **We rely on the journal editor to ensure that
files exist by the time of publication.**

We suggest the following minor edits and recommend the paper be accepted for publication.

- Make a reference to sup. table 5 at the first mention of number of participants and number of
sequence libraries (Findings, line 50-51, page 1)
- Edit figure caption 6 "225 PGP samples" —> "225 PGP genomic libraries"
- Make a reference to sup. table 5 with each figure caption that mentions the 225 genomic
libraries.
- Rephrase the first paragraph in 'LFR specific files' to clarify the deviation from the standard file
structure. Suggested wording: "Relative to the standard file formats (see supplementary material:
Standard Sequencing Service Data File Formats v2.5.pdf) the data packages from LFR do not
include a MEI directory and does not include content in the SV directory. For an overview of the
files and directories included see Figure 2."

Kind regards,

Fiona Nielsen and Richard Shaw

Level of interest
Please indicate how interesting you found the manuscript:

An article of importance in its field .

Quality of written English
Please indicate the quality of language in the manuscript:

Acceptable .

Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of this
manuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
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4. Have you received reimbursements, fees, funding, or salary from an organization that
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If you can answer no to all of the above, write 'I declare that I have no competing interests'
below. If your reply is yes to any, please give details below.

Both Fiona Nielsen and Richard Shaw have previously held employment by Illumina UK (2013
and 2016 respectively).

Both authors declare no current competing interests.

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