Genomic variations (VCF) files

Analyzing the alignments of each rootstock genomic DNA against the reference genome, it is possible to infer the differences between the two. It has to be taken into account that the variability of the coverage across the whole genome – a normal behaviour of any shotgun sequencing experiment – will make each difference more or less probable (accurate).

Here we report the variations found analyzing the BAM files with a custom pipeline involving both samtools mpileup and picard tools. The files are in the standard VCF format.

 

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