3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Subsetting Samples
VcfHeader header;
VcfHeader header;
// Subset 1 is delimited by new lines, '\n'.
// Subset 1 is delimited by new lines, '\n'.
reader.open("vcfFileName.vcf", header, "subsetFile1.txt");
reader.open("vcfFileName.vcf", header, "subsetFile1.txt", NULL, NULL);
</source>
</source>
<source lang="cpp">
<source lang="cpp">
VcfHeader header;
VcfHeader header;
// Subset 2 is delimited by ';'
// Subset 2 is delimited by ';'
reader.open("vcfFileName.vcf", header, "subsetFile2.txt", ';');
reader.open("vcfFileName.vcf", header, "subsetFile2.txt", NULL, NULL, ';');
</source>
To select a subset of samples to remove/ignore, when opening the file also specify the name of the file containing the names of the samples to remove/ignore and the delimiter separating the sample names (default is a new line, '\n').
<source lang="cpp">
// Open the vcf file for reading.
VcfFileReader reader;
VcfHeader header;
// Subset 1 is delimited by new lines, '\n'.
reader.open("vcfFileName.vcf", header, NULL, NULL, "subsetFile1.txt");
</source>
<source lang="cpp">
// Open the vcf file for reading.
VcfFileReader reader;
VcfHeader header;
// Subset 2 is delimited by ';'
reader.open("vcfFileName.vcf", header, NULL, NULL, "subsetFile2.txt", ';');
</source>
If you just have 1 sample to be excluded, you can specify it directly in the open line.
<source lang="cpp">
// Open the vcf file for reading.
VcfFileReader reader;
VcfHeader header;
// Subset 1 is delimited by new lines, '\n'.
reader.open("vcfFileName.vcf", header, NULL, "BAD_SAMPLE", NULL);
</source>
</source>
