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mcfrith / last-genome-alignments

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Call SNPs and INDELs from last results #11

Open Zhuxitong opened 2 years ago

Zhuxitong commented 2 years ago

Dear developers

Do you have any suggestions how I can call SNPs and INDELs from the results of last? In mummer, they provided show-snps and some other scripts for downstream analysis. I wonder if there are some scripts like so or any external tools that you recommand for this purpose?

Very thankful for any suggestions!

mcfrith commented 2 years ago

Sorry I'm not sure of the best answer, but here are some possibilities: https://jydu.github.io/maffilter/ https://github.com/dentearl/mafTools https://galaxyproject.org/main/maf-analysis/ https://biopython.org/wiki/Multiple_Alignment_Format https://github.com/mcfrith/last-genotype

Zhuxitong commented 2 years ago

Hi, @mcfrith, really thanks for you timely reply.

I roughly read the tools you have posted above and found maffilter can be used to call SNPs only and seems other tools are not suitable to call both SNPs and INDELs.

I think out a way for such purpose but have not try it. Basic flows are:

1, convert maf to sam using maf-convert; 2, call variants using samtools and vcftools pipeline.

I am not sure if this works or not, I will try it and have a check in IGV or some small region obtained by maffilter or mafTools:)