Some sites were deleted

[tydcg]

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]

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]

Hi，

How to change the ALT for reserving the InDel sites?

[hewm2008]

@prometheusloong you can see at this : #7