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, 16:57, 25 July 2012
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| VcfFileReader::rmDiscardMinAltAlleleCount() | | VcfFileReader::rmDiscardMinAltAlleleCount() |
| </source> | | </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 ===== | | ===== Minimum Minor Allele Count ===== |
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| VcfFileReader::rmDiscardMinMinorAlleleCount() | | VcfFileReader::rmDiscardMinMinorAlleleCount() |
| </source> | | </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 ==== | | ==== Read only Certain Sections of the File / Using a VCF Index (TABIX) File ==== |