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Add a script to add chr-pos-ref-alt to input files with only rsid #66

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sgagliano opened this issue Apr 3, 2017 · 2 comments
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@sgagliano
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For association results with rsID only, add a script to map the variants to chr:bp (b37).

@pjvandehaar pjvandehaar reopened this May 18, 2017
@pjvandehaar
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pjvandehaar commented May 18, 2017

Approaches:

  • a file tabixed by rsid
    • if the rsid-only file is sorted by rsid, we could hold the last tabixed block in a cache (maybe even in a dictionary?)
  • a bgzip file sorted by chr-pos with a [hash(rsid) -> bgzip block] index
    • if our rsid-only file is actually sorted by chr-pos (despite not having them), we could hold the last successful bgzip block as a cache.
  • a sqlite3 table
    • see /net/snowwhite/home/welchr/projects/dbsnp/make_sqlite_db.py

@pjvandehaar pjvandehaar changed the title rsIDs, no chr:bp convert rsid -> chr-pos-ref-alt May 19, 2017
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(replaces #43)

@pjvandehaar pjvandehaar changed the title convert rsid -> chr-pos-ref-alt Add a script to add chr-pos-ref-alt to input files with only rsid Feb 16, 2021
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