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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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How do I know the structural variations from the output of cactus? #578

Open Chenglin20170390 opened 2 years ago

Chenglin20170390 commented 2 years ago

Hi， 1) after doing multiple genome alignment (reference, A, B, C and D genome). I want to know the information of SNP and SV in the alignment compared with the reference genome position(like vcf file). Do you have any suggestions?
2 ) I would like to find synteny region (only reference, A, B, C and D genome )from the output of cactus, can you give me some advice? from the output maf file, sometimes, I can see reference, A, B and D，but no C genome)

by the way, do you have more documents about how to deal with hal file from the output of the cactus?

many thanks

glennhickey commented 2 years ago

There is a little bit of information on finding mutations (in BED format) here: https://github.com/ComparativeGenomicsToolkit/hal

Not mentioned there is halSynteny which may help you with your second point.

aminakur commented 1 year ago

Hi @Chenglin20170390 were you able to solve your second problem? It seems like halSynteny can only find blocks of synteny between two genomes.