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LibStatGen: VCF

1,410 bytes added, 15:57, 25 July 2012
Specifying Discard Rules
VcfFileReader::rmDiscardMinAltAlleleCount()
</source>
 
Example: Minimum Alternate Allele Count = 4
Sample1 Sample2 Sample3 Keep/Discard
0|0 1|1 2|2 Keep
0|0 0|1 2|2 Discard, only 3 Alternates (1 Allele1 & 2 Allele 2)
0|0 1|1 1|2 Keep
0|2 1|1 2|2 Keep
2|1 0|1 2|0 Keep
 
Example: Minimum Alternate Allele Count = 3 & Exclude Sample2 (without the exclusion, all would be kept)
Sample1 Sample2 Sample3 Keep/Discard
0|0 1|1 2|2 Discard, only 2 Alternates (0 Allele1 & 2 Allele 2)
0|0 0|1 2|2 Discard, only 2 Alternates (0 Allele1 & 2 Allele 2)
0|0 1|1 1|2 Discard, only 2 Alternates (1 Allele1 & 1 Allele 2)
0|2 1|1 2|2 Keep
2|1 0|1 2|0 Keep
 
===== Minimum Minor Allele Count =====
VcfFileReader::rmDiscardMinMinorAlleleCount()
</source>
 
Example: Minimum Minor Allele Count = 2
Sample1 Sample2 Sample3 Keep/Discard
0|0 1|1 2|2 Keep
0|0 0|1 2|2 Discard, only 1 Allele1
0|0 1|1 1|2 Discard, only 1 Allele2
0|2 1|1 2|2 Discard, only 1 Allele0
2|1 0|1 2|0 Keep
 
Example: Minimum Minor Allele Count = 1 & Exclude Sample2 (without the exclusion, all would be kept)
Sample1 Sample2 Sample3 Keep/Discard
0|0 1|1 2|2 Discard, 0 Allele1
0|0 0|1 2|2 Discard, 0 Allele1
0|0 1|1 1|2 Keep
0|2 1|1 2|2 Discard, 0 Allele1
2|1 0|1 2|0 Keep
==== Read only Certain Sections of the File / Using a VCF Index (TABIX) File ====

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