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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.
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.
There are additional discard rules that can be specified by calling methods on VcfFileReader.
</source>
</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 specified subset (if specified) in order for the record to be kept.
The <code>minAltAlleleCount</code> parameter is the minimum number of alternate alleles found in the subset in order for the record to be kept.
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.
To specify a <code>VcfSubsetSamples</code> use the constructor:
<source lang="cpp">
void VcfSubsetSamples::init(const VcfHeader& header, bool include)
</source>
Pass in the header that was read from the VCF file. Set <code>include</code> to true if all samples should be included 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 samples.
To 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:
Use the following method to remove the DiscardMinAltAlleleCount rule:
