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aineniamh / snipit

snipit: summarise snps relative to your reference sequence
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Added option to visualise indels in the snipit plot #9

Closed charlesfoster closed 2 years ago

charlesfoster commented 3 years ago

snipit plots normally discard most indel information. An exception is a site where there is a SNP in one sample compared to the reference, and a deletion in one or more other sequences. In that case, the deletions show up in grey. This PR adds the option to visualise indels using a new --include-indels flag (the default is False, thereby excluding indels). I found this option useful for recent publications where we are exploring the effects of certain deletions. The new option can be used like so:

  1. snipit alignment.fa -o snipit_no_indels -c primary -f pdf -r reference

image

  1. snipit alignment.fa -o snipit_with_indels -c primary -f pdf -r reference --include-indels

image

I tried to choose colours for gaps that fit in with the existing colour schemes.

aineniamh commented 2 years ago

I'm so sorry, I completely missed this PR! I had recently started trying to include indels myself (https://github.com/aineniamh/snipit/tree/indel_dev), and I'll have a look through both changes and merge them this week!