[PRE REVIEW]: cerebra: A tool for fast and accurate summarizing of variant calling format (VCF) files

[whedon]

Submitting author: @lincoln-harris (Lincoln Harris) Repository: https://github.com/czbiohub/cerebra Version: v1.1.0 Editor: @lpantano Reviewers: @betteridiot, @afrubin Managing EiC: Kristen Thyng

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

Thanks for submitting your paper to JOSS @lincoln-harris. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @lpantano.

@lincoln-harris if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1093/bioinformatics/btl647 may be missing for title: Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases
- https://doi.org/10.1093/bioinformatics/btp324 may be missing for title: Fast and accurate short read alignment with Burrows-Wheeler Transform
- https://doi.org/10.1016/j.cell.2017.09.004 may be missing for title: Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns
- https://doi.org/10.1038/s41587-019-0074-6 may be missing for title: An open resource for accurately benchmarking small variant and reference calls
- https://doi.org/10.1038/nbt.2835 may be missing for title: Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
- https://doi.org/10.1101/201178 may be missing for title: Scaling accurate genetic variant discovery to tens of thousands of samples
- https://doi.org/10.1186/s13059-017-1248-5 may be missing for title: BRIE: transcriptome-wide splicing quantification in single cells

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.20 s (243.8 files/s, 33401.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          23            820            639           2034
RobotFramework                   1              0              0           1400
Markdown                         7            222              0            592
make                             3             73             53            291
DOS Batch                        1             29              1            212
YAML                             3              1              0            150
TeX                              1             10              0             68
reStructuredText                 9             36             29             48
Dockerfile                       1              2              0              4
-------------------------------------------------------------------------------
SUM:                            49           1193            722           4799
-------------------------------------------------------------------------------

Statistical information for the repository '2396' was gathered on 2020/06/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Lincoln Harris                 161         11421           9338           78.62
Olga Botvinnik                   1             1             15            0.06
Rohan Vanheusden                73          2785           1038           14.48
Ubuntu                          32           888            919            6.84

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Lincoln Harris             1941           17.0          1.9               18.39
Olga Botvinnik                1          100.0          1.3                0.00
Rohan Vanheusden           1551           55.7         10.7                9.09

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kthyng]

Hi @lincoln-harris!

Thanks for your submission to JOSS. As described in our blog post announcing the reopening of JOSS, we're currently working in a "reduced service mode", limiting the number of papers assigned to any individual editor.

Since reopening JOSS earlier in the month we've had a very large number of papers submitted and as such, yours has been put in our backlog that we will be working through over the coming weeks and months.

Thanks in advance for your patience!

[lpantano]

@kthyng, I can edit that if you don't have another person in mind :)

[kthyng]

Sounds great @lpantano! Thanks!

[kthyng]

@whedon assign @lpantano as editor

[whedon]

OK, the editor is @lpantano

[lpantano]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1093/bioinformatics/btl647 may be missing for title: Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases
- https://doi.org/10.1093/bioinformatics/btp324 may be missing for title: Fast and accurate short read alignment with Burrows-Wheeler Transform
- https://doi.org/10.1016/j.cell.2017.09.004 may be missing for title: Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns
- https://doi.org/10.1038/s41587-019-0074-6 may be missing for title: An open resource for accurately benchmarking small variant and reference calls
- https://doi.org/10.1038/nbt.2835 may be missing for title: Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
- https://doi.org/10.1101/201178 may be missing for title: Scaling accurate genetic variant discovery to tens of thousands of samples
- https://doi.org/10.1186/s13059-017-1248-5 may be missing for title: BRIE: transcriptome-wide splicing quantification in single cells

INVALID DOIs

- None

[lpantano]

@lincoln-harris, can you make sure all the references has DOI, please?

[lpantano]

@chrisleitzinger, I found your profile in GitHub and I thought you may be interested on reviewing this nice VCF reader tool. This are the guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html. Thanks!

[lpantano]

hey @naumenko-sa, I think you may be interested in reviewing this tool? let me know!

[lpantano]

hey @Adrianzo, @afrubin, @betteridiot, @Nazeeefa, would any of you like to review this paper?

[betteridiot]

I would be happy to review this @lpantano

[afrubin]

@lpantano Happy to review this as well.

[lpantano]

@whedon assign @betteridiot as reviewer

[whedon]

OK, @betteridiot is now a reviewer

[lpantano]

@whedon add @afrubin as reviewer

[whedon]

OK, @afrubin is now a reviewer

[lpantano]

Thanks both, I will start the review process then!

[lpantano]

@whedon star review

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[lpantano]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2432.

[Nazeeefa]

Hi, I'd be happy to review/test it @lpantano

[lpantano]

Hi @Nazeeefa, I got two reviewers here, but I need one more for this other tool: https://github.com/openjournals/joss-reviews/issues/2410 would you be up for that one? It is a visualization tool of metabolomic data. It would be great to have you there!

[Nazeeefa]

Hi @lpantano No worries. Sorry, I'm afraid I have to say no as I do not know much about that topic. Thank you for asking. I appreciate your time and work.