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BGI-shenzhen / PopLDdecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
MIT License
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Structure Variation #20

Open lunky-zao opened 9 months ago

lunky-zao commented 9 months ago

when I use a vcf with structure variation, It's warning skip Indel site, there are total skip Indel sites number is : 618346，after filter Remain SNP Number : 0. Does it mean that VCF files with structural variations cannot be used with this software?

hewm2008 commented 9 months ago

yes. A ：The soft will skip non bi-allelic(Singleton/ThreeMulti allelic) site and indel site (For bi-allelic indel, you can modify the "REF ALT" to only one base. see the Perl script at the end of this conversation

I provide a script here that can change bi-allelic indel to SNP, which can be reserved for calculation https://github.com/BGI-shenzhen/LDBlockShow/issues/7