User: silvia.shuchang.liu

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Posts by silvia.shuchang.liu

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Answer: A: How to set genotypes with low GQ to missing. in a vcf file.
... You can use vcftools '--minGQ' option for genotype quality filtering > vcftools --vcf a.vcf --minGQ 90 --out b --recode A b.recode.vcf file will be generated. Please check man vcftool for details, https://vcftools.github.io/man_latest.html ...
written 11 months ago by silvia.shuchang.liu10
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Answer: A: Error running smartpca from eigensoft
... Since example.evec should be an output from smartpca step, and its the input for evec2pca.perl step. But for smartpca.perl, there is no where to set this argument, so the second step cannot find example.evec. I suggest you to use the steps separately, $../POPGEN/example.perl smartpca -p par.exampl ...
written 11 months ago by silvia.shuchang.liu10

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