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bias towards the ref allele in Haplotypecaller

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Hi,
I've been calling SNPs of more than 10 DNAseq libraries in Arabidopsis and always get a strong bias in the number of calls for the reference allele (2-10 fold). I thought that HC might see errors as snps and that might create such bias but it doesn't seem to be the case.

Thanks a lot,
Guy


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