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asterisk in phylip file

Dear all: There were so many asterisk (*) in my output phylip sequences when I converted a vcf file into phylip format using vcf2phylip. Can anybody help solve this problem? Thank you

vcf2phylip asterisk
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written by Chenfei Zheng Chenfei Zheng

Please provide a sample from your file so we can understand what you are talking about.

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written by liorglic liorglic

1 answer

It looks like "*" represents a gap "-".

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written by Klaus S Klaus S

Thank you for your reply. This "" can not be identified by following programs like iqtree. I've tried to remove those snp positions in vcf file, but new "" always arise after old ones were deleted. Do you know how to fix this? Thank you.

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written by Chenfei Zheng Chenfei Zheng

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