Use tabix when splitting imputation server vcfs#60
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robkar wants to merge 1 commit intoRipkelab:masterfrom
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Use tabix when splitting imputation server vcfs#60robkar wants to merge 1 commit intoRipkelab:masterfrom
robkar wants to merge 1 commit intoRipkelab:masterfrom
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As discussed in emails with Stephan. Using the new --deploy option for pre- and postprocessing imputation server files, I found the conversion from chromosomal vcfs to dosage chunks too slow in some cases.
I updated the scripts to use tabix for deployed imputation files with indices, which improved performance substantially (now my problematic chunks finish before the cluster kills them).
The logic I wrote stops with an error if using --deploy and there are no index files (I think both Sanger and Michigan provide them?), but for other uses of vcf2dos (i.e. in-house imputation), the script should proceed by reading the full file if there is no index.