User: dario.galanti92

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Posts by dario.galanti92

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Comment: C: How Can I Count Snps In My Final Vcf Files
... Yes, that was indeed wrong, apologies. I fixed it now. ...
written 5 weeks ago by dario.galanti920
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Answer: A: How Can I Count Snps In My Final Vcf Files
... Here is a quick way to count **biallelic** SNPs in vcf.gz files (use "cat" instead of "zcat" for uncompressed vcf files): zcat input.vcf.gz | awk '{if ($4~/^[ACGT]$/ && $5~/^[ACGT]$/){c++}} END {print c}' ...
written 5 weeks ago by dario.galanti920
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Answer: A: Minimum # markers per chromosome/scaffold for imputation with Beagle 5.1
... Solved it! I removed all scaffolds harbouring less than 3 SNP in my vcf file and it worked smoothly! Good luck to anyone else having the same problem! ...
written 10 months ago by dario.galanti920
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Minimum # markers per chromosome/scaffold for imputation with Beagle 5.1
... I have a multisample vcf file from a study species with a pretty fragmented reference genome. I already applied the basic filtering steps to my vcf using vcftools. 1- Sample filtering: filter out low coverage samples 2- Site and genotype filtering with the following vcftools parameters: --minDP 3 -- ...
vcf imputation snp beagle written 10 months ago by dario.galanti920

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