Zamin Iqbal

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Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

Cc @Danderson123

Clinker producing "blank" plot for 2 identical sequences

sorry, i don't understand why I didn't get a notification for your message. will chase up and get examples

0 depth reported across many genes in the pandora consensus

Just a reminder we need a small example

0 depth reported across many genes in the pandora consensus

ping @Danderson123

Request for new release

Spoke to leandro about this this morning! We suggested a call when you back from holiday

Cortex calling regions with no reads as indels

Hi there, coukd you show me the cortex call associated with those last 2 pileups? Are you saying cortex calls an indel which is not the deletion one would infer...

Cortex calling regions with no reads as indels

Sorry for slow reply, will discuss with @martinghunt on Monday

Cortex calling regions with no reads as indels

yes agree! Cortex will have assembled a long allele and the reads don't map to the reference so it looks like a deletion from the bam. Martin's idea of switching...

Cortex calling regions with no reads as indels

Hi there A few things 1. When you replace the ref-allele with the alt-allele for that long variant, and then map reads, how good does the depth look? does it...

Cortex calling regions with no reads as indels

Right - we've had some conversations offline also, let me summarise my understanding. 1. **The cortex calls look correct** - these are regions which are highly diverged from the reference,...