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, 12:28, 20 January 2016
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| I am trying to make vt handle [http://genome.sph.umich.edu/wiki/Relationship_between_Ploidy,_Alleles_and_Genotypes general cases of ploidy and alleles]. | | I am trying to make vt handle [http://genome.sph.umich.edu/wiki/Relationship_between_Ploidy,_Alleles_and_Genotypes general cases of ploidy and alleles]. |
| Please let me know if that is lacking in a tool that you are using. | | Please let me know if that is lacking in a tool that you are using. |
| + | |
| + | == BCF Compression vs Compression Time == |
| + | |
| + | The zlib deflation algorithm (a variant of LZ77) has 10 levels - 0 to 9. 0 has no compression but instead wraps up the file in zlib or bgzf blocks. |
| + | Levels 1-9 denote an increasing compression level in exchange for longer times for compression. |
| + | |
| + | In general, zlib compression does not have significant difference in compression between the 9 compression levels as shown in the following table: |
| + | |
| + | {| class="wikitable" |
| + | |- |
| + | ! scope="col"| Compression Level |
| + | ! scope="col"| Size |
| + | ! scope="col"| Time |
| + | |- |
| + | |0 <br> |
| + | 1 <br> |
| + | 6 (default) |
| + | | 153GB <br> |
| + | 99GB <br> |
| + | 95GB |
| + | | 25m<br> |
| + | 2h1m <br> |
| + | 3h16m |
| + | |} |
| | | |
| = VCF Manipulation = | | = VCF Manipulation = |