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Liftover variants/vcf called on NCBI reference genome

Could you use the hg19 --> hg38 chain from here? As I understand it, the main difference between GrCH37 and hg19 are the format the chromosomes are written (whether there is a "chr" ...
Sarah's user avatar
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1 vote

Liftover variants/vcf called on NCBI reference genome

Liftover is hard. While many variants can be lifted over relatively easily, some cannot. First, some variants are not even variants in the other genome (the other genome has the variant allele as the ...
terdon's user avatar
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1 vote

How to extract mutations in a particular gene from the VCF file of whole genome

As mentioned, there are many options to go (eg. vcftools and bcftools). The Broad Institute provides a valuable toolset (GATK) for this very purpose and extended procedures for various variant ...
44Pasha's user avatar
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1 vote

How to extract mutations in a particular gene from the VCF file of whole genome

Find the location of the gene of interest and then filter the vcf for that location using vcftools, bcftools, plink, or some other software. There is a lot of good documentation available online for ...
Sarah's user avatar
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1 vote

How can I filter variants in a VCF file based on size?

Vcftools allows you to filter to include or not include a list of sites. https://vcftools.github.io/man_latest.html#SITE%20FILTERING%20OPTIONS If you can first grab the locations of indels of this ...
Sarah's user avatar
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How should multi allelic sites be handled in calculation per site Fst?

Hmmmm .... I personally would not use a single VCF to calculate Fst in the way you are describing. It will also miss one of the nucleotides. I would aggregate across VCFs for a homologous position and ...
M__'s user avatar
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