I'm wondering if there is a way how to copy consensus sequence from many chromosomes at once?
I can select chromosome one by one and for each of them right click to "Copy consensus sequence", however since I'd like to get the consensus for hundreds of "chromosomes" (in my case actually genes which I used as reference for construction of my bam file) it is not feasible to perform it manually "chromosome-by-chromosome".
The "copy consensus sequence" functionality implemented in IGV is, I believe, quite unique as it reports the type of consensus which might be otherwise impossible (or complicated) to retrieve by other tools for extracting consensus from bam files (e.g. I failed to fine-tune the criteria for extracting consensus using combination of samtools mpileup, bcftools and vcfutils which is typically used to get the consensus). Therefore I believe it would be cool if there is an option (or possibly trick/workaround) how to copy in IGV consensus for many "chromosomes" at once.
Thanks for any hints.