Closed bschilder closed 3 years ago
This is now implemented when write_vcf=TRUE
.
To do: Implement for tabular format as well.
Now implemented for tabular output format. The index_tabular
function is also exported in case users want to index their sum stats later on:
https://github.com/neurogenomics/MungeSumstats/blob/bschilder_dev/R/index_tabular.R
New tests for this function are here: https://github.com/neurogenomics/MungeSumstats/blob/bschilder_dev/tests/testthat/test-index_tabular.R
I've also added the necessary checks in check_save_path
to ensure the output filename ends with ".bgz":
https://github.com/neurogenomics/MungeSumstats/blob/8ab84dc6e5195eb30dbd95f18ada0f03c1bbd362/R/check_save_path.R#L114
Tabix indexing makes querying your sum stats extremely efficient, with minimal changes to the format.
seqminer has a number of functions to do this within R. I've also written a bunch of command line wrappers to do these things in echolocatoR.