Comparing 2 MAF files for differences when generated using different genome builds

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4.8 years ago

b.issac74 • 0

Hi

This is probably a basic question, but I did not find a similar question in the forum.
Is there a way to compare 2 MAF files that was generated for same data, but was generated using hg19 and hg20 respectively?

Thanks
-BumbleBee

snp • 858 views

ADD COMMENT • link updated 4.8 years ago by WouterDeCoster 47k • written 4.8 years ago by b.issac74 • 0

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Is this the MAF variant format or the MAF alignment format?

If variants: What you are looking is called LiftOver. I don't know if it exists for MAF format though, I am sure it does exist for VCF.

ADD REPLY • link 4.8 years ago by WouterDeCoster 47k

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Thanks

its Variants. However, I am looking to compare the files after the liftover step. Just wanted to know if anyone already has a running script or do I custom build this

ADD REPLY • link 4.8 years ago by b.issac74 • 0

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