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Published 20 hours ago • verified publisher icon BGI-shenzhen

Some sites were deleted

Open tydcg opened this issue 11 months ago • 3 comments

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！

tydcg avatar Mar 14 '24 09:03 tydcg

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

hewm2008 avatar Mar 15 '24 01:03 hewm2008

Hi，

How to change the ALT for reserving the InDel sites?

prometheusloong avatar Aug 27 '24 04:08 prometheusloong

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

hewm2008 avatar Aug 28 '24 01:08 hewm2008