Illumina/paragraph

Which aligner?

fergsc opened this issue · 2 comments

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.

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

Thanks