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Illumina / paragraph

Graph realignment tools for structural variants
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Which aligner? #56

Closed fergsc closed 3 years ago

fergsc commented 4 years ago

Hi, I am just starting to investage using Paragraph to genotype some SV within a number of poulations. I shall be doing a lot of alignments of short reads to my references. Is there a preferred aligner to use to generate the bam file for input into paragraph?

thanks.

traxexx commented 3 years ago

No preference for aligners. As long as the input BAM is valid and matches your input reference fasta.

fergsc commented 3 years ago

Thanks