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low quality variants
is there a way to output all possible variants (the alternate allele)? i have total reads of 2100 whereby 2045 reads are match reference and 55 reads are alternate allele. My case is very specific, i would like GATK UnifiedGenotyper to call out my variants although the proportion of alternate read is relative low (1-5%) . And regardless of the quality score of alternate reads. Is there a way to specify this settings during the SNP calling in GATK UnifiedGenotyper?
thank you very much