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623 bytes added, 12:28, 20 January 2016
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.
 
== 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 =
1,102
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