User: mek362

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mek36210
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Posts by mek362

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Calculating FST from Transcriptomic Sequence Data stored in a VCF
... Hi all, I am working with *de novo* - assembled transcriptomes, and would like to estimate a suite of neutrality and F stats for each locus (i.e. contig) using sequence variation (as opposed to SNPs). So far, I have used the R package PopGenome to estimate single-population and pairwise FST, as we ...
de novo popgenome fst sequence data rna-seq written 3.0 years ago by mek36210
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Comment: C: Filter VCF on Number of genotyped individuals
... Thanks for the answer, Brice. This worked well -- I split the master .vcf by population, filtered using vcftools --recode, and merged filtered population .vcf's using bcftools isec. It may also be useful to note that the --max-missing option excludes sites based on proportion of missing data, where ...
written 3.0 years ago by mek36210
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Filter VCF on Number of genotyped individuals
... Hello all, I would like to know how to filter a VCF by number of individuals with genotype data (i.e. without missing data). First, some background: I have a large VCF file containing SNP data for 95 individuals called from bcftools mpileup output. BAMs passed to mpileup contained data for ali ...
vcf snp filtering transcriptome written 3.0 years ago by mek36210 • updated 3.0 years ago by Brice Sarver2.8k

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