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BGI-shenzhen / LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
MIT License
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Some sites were deleted #40

Open tydcg opened 7 months ago

tydcg commented 7 months ago

微信图片_20240314165254 Hi, I found some SNP/Indel sites were filtered, can I rescue them by certain parameters? And I want to calculate LD of rare variants, setting "-MAF 0", but this parameter doesn't seem to work? Please give me some guidance. Thank you！

hewm2008 commented 7 months ago

Maf 不可以为0 。为0就不是snp 了。可以保留 中低频的，你若是最新版本 看看打印在拼幕的信息 会洗哪个条件过滤多少位点.若是bi-allele 的indel 可以改一下ALT 即可以保留

prometheusloong commented 2 months ago

Hi，

How to change the ALT for reserving the InDel sites?

hewm2008 commented 2 months ago

@prometheusloong you can see at this : https://github.com/BGI-shenzhen/LDBlockShow/issues/7