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LibStatGen: VCF

739 bytes added, 10:27, 24 July 2012
Specifying Discard Rules
==== Specifying Discard Rules ====
===== Basic Rules =====
When specifying the discard rules, you should use the constants found at the top of VcfFileReader.h
</source>
and discards reads that do not have <code>PASS</code> in the <code>FILTER</code> field and reads that have a genotype that is not phased or have no <code>GT</code> in the <code>FORMAT</code> fields.
 
===== Additional Rules =====
There are additional discard rules that can be specified by calling methods on VcfFileReader.
 
To Discard any records without a minimum number of alternate alleles, use:
<source lang="cpp">
VcfFileReader::addDiscardMinAltAlleleCount(int32_t minAltAlleleCount, VcfSubsetSamples* subset)
</source>
 
The <code>VcfSubsetSamples* subset</code> parameter is a pointer to the subset of samples that you want to include when counting the number of alternate alleles. If all samples that are read/kept are to be included, NULL should be passed in.
 
The <code>minAltAlleleCount</code> parameter is the minimum number of alternate alleles found in the subset in order for the record to be kept.
==== Read only Certain Sections of the File / Using a VCF Index (TABIX) File ====

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