User: zhangdezhi008

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Posts by zhangdezhi008

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Comment: C: How to interpret genotypes with DP=1 for a vcf file
... Thanks for your reply. I will not trust the lower DP SNPs. How can one read possesses an alternative base? I also have another question, how can we know the depth for each allele for a heterozygous site? ...
written 4 days ago by zhangdezhi0080
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How to interpret genotypes with DP=1 for a vcf file
... Dear all, I used samtools for SNPs calling and vcftools for SNPs filtering. I got a vcf file with a lot SNPs.How to interpret the genotypes when DP=1? In my opinion, DP=1 means that this site has only one read, it could be homozygous 0/0 or 1/1, but how can it be a heterozygous 0/1? The following i ...
next-gen snp sequencing written 4 days ago by zhangdezhi0080 • updated 4 days ago by b.nota2.9k
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Comment: C: How to delete two populations pseudo snps from a mutiple populations vcf file?
... Hi Pierre, If using mutlple populations to call SNPs, but only paired comparison are needed, there may have some sites are not SNPs anymore. And also, using multiple populations would omit biallelic SNPs only exist in the focal two populations, because these kind SNPs may become triallelic or tetra ...
written 3 months ago by zhangdezhi0080
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How to delete two populations pseudo snps from a mutiple populations vcf file?
... Hi all, I used three populations to call snps by SAMtools.And filtered biallelic snps by vcftools, I need to calculate between populations's fst, the original vcf file was divided into 3 sub-vcf files, each sub-vcf only contains two populations. The variant sites exist in the original vcf for t ...
genome snp sequencing written 3 months ago by zhangdezhi0080 • updated 6 weeks ago by Biostar ♦♦ 10

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