How to write a batch script for IGV that directly leads me to my chosen SNPs on certain BP range on each chromosome

Hello humans,

as input for the script I have a list of BP ranges on several chromosomes and I am wondering how to write an IGV script that directly leads me only to these areas, without showing the whole chromosomes.

Thanks for your help in advance

Input:

Chr xy1 BP-start  BP-end, 
Chr xy1 BP2-start BP2-end, 
Chr xy2 BP1-start BP1-end, 
Chr xy2 BP2-start BP2-end,

batch igv script snp

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updated 4.5 years ago by Pierre Lindenbaum

• written 4.5 years ago by Human •

Running IGV with a batch file

https://software.broadinstitute.org/software/igv/batch

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written 4.5 years ago by Pierre Lindenbaum

cross-posted: https://stackoverflow.com/questions/71234648/

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written 4.5 years ago by Pierre Lindenbaum

1 answer

This tool is likely useful:

https://github.com/igvteam/igv-reports

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written 4.5 years ago by colindaven

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