Bwa single end reads

GATK* - Genome Analysis Tool Kit*

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A reference genome for pea provides insight into legume genome evolution

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Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

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It can also be compressed to create BCF format to save space. Unlike the mpileup format, which showed one line for every base in the genome at which we had beats alike. The VCF format gives detailed information about only those positions at which we mark variation, we identify variation. So as you can see here, it is a fairly dense file that starts in a file beginning with a preamble. We recognize the preamble because every line starts with two signs.

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