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I chose a set of human samples with a common haplotype for illumina resequencing, and targeted the haplotype locus with a capture chip. I would like to call the variants which most of these samples share in this haplotype locus. Are there any bioinformatics packages which would help me to do this in an intelligent way?
One obvious thing to do is to pool the reads which align to the haplotype locus into a bam file, and do a pileup from that. But I would prefer a method which took into account which reads came from which samples and gave higher weight to variants which appear in a significant fraction of the samples.
One obvious thing to do is to pool the reads which align to the haplotype locus into a bam file, and do a pileup from that. But I would prefer a method which took into account which reads came from which samples and gave higher weight to variants which appear in a significant fraction of the samples.