This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Can GATK score known SNPs from an individual alignment file?
I have recently generated a list of known SNPs from two closely related species, and am now looking to score each SNPs within each individual from my study (i.e. generate a SNP haplotype for each individual). Are there functions within GATK for scoring a list of known SNPs for an individual. Keep in mind that some sites will be homozygous for for some individuals, even if they are polymorphic overall.
My data is presently in the form of BAM files, but can readily be converted to SAM files, mpileup files, etc.
I have read the documentation for the Haplotype and Unified Genotypres, but am still unsure if this is possible.