`format_sumstats()` fails to infer genome build about mungesumstats HOT 2 CLOSED

Thank you for fixing this bug so quickly! The updated version now works correctly on my example GWAS file.

As for rearranging the QC checks, I can see why doing so would be more complicated than I initially imagined. I'll let you know if I run into any other GWAS formats that break get_genome_build().

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Hey! Thanks for the detailed report. Some things to note:

Moreover, I think that get_genome_build() should fail if no matches are found, rather than defaulting to GRCh38 (which is the current behavior).
I agree, I have added this fix - if no match is found in either genome build MSS will now fail.

incorrectly concludes the reference genome for a GWAS summary statistics file that has chromosome numbers coded with the "chr" prefix
I have added a check for this in the check genome build function so it should work as expected now but let me know if it doesn't?

Instead, I suggest rearranging the QC steps in format_sumstats() to put all QC steps that don't rely on the GWAS assembly before the call to get_genome_build()
I had a look through all our 60+ checks and the vast majority require a genome reference. Moreover, these checks are interdependent so even if a check itself doesn't require a genome reference, a check it relies on might. This gets quite complicated so I have avoided moving any checks for SNP, CHR and BP to above the inference of genome build for now. However, do let me know if you come across any other examples other than the 'CHR' prefix which causes an issue with inferring the genome build and I'll be happy to update.

These changes have been added to MSS v1.9.9. You can install this from Github now or wait a few days for it to go up on the devel version of Bioconductor. Let me know if your issue persists (feel free to reopen this issue if so).

Cheers,
Alan.

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