Ryan Welch

You'll need to use the sample size weighted meta-analysis `SCHEME SAMPLESIZE`, and specify `WEIGHT` (sample size column) and `PVALUE` (p-value column). The [documentation](https://genome.sph.umich.edu/wiki/METAL_Documentation#Selecting_an_Analysis_Scheme) has more information on the analysis methods...

That error looks to only occur in two places in the program: https://github.com/statgen/METAL/blob/e2253cc3901df8403a331bd725d4d9fe1edfb19f/metal/Main.cpp#L1807-L1809 https://github.com/statgen/METAL/blob/e2253cc3901df8403a331bd725d4d9fe1edfb19f/metal/Main.cpp#L2158-L2160 Seems to always have something to do with the number of separate tokens it can find...

If you change `proccess` -> `process` for the final file, does it work?

Does `which libtoolize` show that it's on your PATH? If so, does re-running `autoreconf -vfi` and then `./configure` work?

Beagle appears to have created an hg38 recombination map: http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/ Unfortunately, I can't find any documentation on how this was produced (is it a liftover of the previous maps?) We...

These are the recombination rates we are using for hg38: http://csg.sph.umich.edu/locuszoom/download/recomb-hg38.tar.gz You will need to update your database file, see `README.md` for information on how to do that. We may...

Looks like where they switch back to 0 are the starting positions of the two PAR regions on chrX. In the original files, they are `plink.chrX_par1.GRCh38.map` and `plink.chrX_par2.GRCh38.map`.

Unfortunately I think LocusZoom requires chrX or chr23, it probably wouldn't work with differently named versions of chrX (like chrX-PAR1, etc.) If you're not using the file with LocusZoom, though,...

You could check and see if anything actually got inserted into the table: ```bash echo 'select * from recomb_rate limit 10' | sqlite3 data/database/locuszoom_hg38.db ```

Try putting the following: ```c++ #include ``` Into the files `filter.h` and `hts_utils.h`.