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LibStatGen: VCF

818 bytes added, 10:42, 24 July 2012
Additional Rules
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 Minimum Alternate Allele Count =====
There are additional discard rules that can be specified by calling methods on VcfFileReader.
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The <code>VcfSubsetSamples* subsetminAltAlleleCount</code> parameter is a pointer to the subset of samples that you want to include when counting the minimum number of alternate alleles. If all samples that are read/kept are found in the specified subset (if specified) in order for the record to be included, NULL should be passed inkept.
The <code>minAltAlleleCountVcfSubsetSamples* subset</code> parameter is a pointer to the subset of samples that you want to include when counting the minimum number of alternate alleles found . If all samples that are read/kept are to be included, NULL should be passed in .  To specify a <code>VcfSubsetSamples</code> use the subset constructor:<source lang="cpp">void VcfSubsetSamples::init(const VcfHeader& header, bool include)</source>Pass in order for the record header that was read from the VCF file. Set <code>include</code> to true if all samples should be keptincluded except any that are specified as excluded. Set <code>include</code> to false if all samples should be excluded except any that are specified as included. NOTE: the header is not modified to add/remove any samplesTo mark a specific sample as excluded use:<source lang ="cpp">bool VcfSubsetSamples::addExcludeSample(const char* sampleName);</source>To mark a specific sample as included use:<source lang ="cpp">bool VcfSubsetSamples::addIncludeSample(const char* sampleName);</source>
Use the following method to remove the DiscardMinAltAlleleCount rule: