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tobiasrausch / alfred

BAM Statistics, Feature Counting and Annotation
https://www.gear-genomics.com/alfred/
BSD 3-Clause "New" or "Revised" License
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A question of the example shell of the Haplotype-specific #71

Closed MMengrui closed 2 years ago

MMengrui commented 2 years ago

Hi Tobias I have a question of the example shell in the software folder. 企业微信截图_16418016297093 When you convert the vcf file to the bcf format, you use the parameter (-m2 -M2 -c 1 -C 1) to filter some variant sites. It seemed that this parameter would retain the variant sites of 0/1 type. Why you use this parameter?

tobiasrausch commented 2 years ago

When you want to split the data by haplotype only heterozygous variants (0/1) are informative for a diploid sample.

MMengrui commented 2 years ago

I got it. Thank you very much!