Hello,
I read in a recently published article that 'Homeologous SNPs identified from each genotype were eliminated using VCFtools'. Can anyone shed some light on which filtering option in the VCF tools would do that?
Thanks in advance.
Regards
Swati
•
written
by
swatipuraanik •
1 answer
The --diff command of VCFtools with --diff-site flag is used to compare VCFs and report unique variants.
Edit: it appears that you want to filter non-homozygous SNPs within a polyploid genome; correct? If so, you can filter by read depth, minimum allele frequency, and minimum quality as described in this publication.
VCF files were first filtered for depth (four reads per genotype covering base of interest) using a custom python script. Then vcftools (Danecek et al. 2011) was run with the following parameters: "–maf 0.35–minQ 30–remove-filtered-all–remove-indels –recode."
Log in to answer this question.
-
VCFtools + easySFS snp # discordance
written by laurasachica7 •
-
Polyploidy found, and not supported by vcftools for a diploid data set.
written by Shripathi •
-
Output bigger than input. VCFtools
written by victor.agrs •
-
compare and merge VCF files
written by qwzhang0601
-
How can I convert heterozygous genotype data to missing data?
written by recycled8345 •
-
Filtering specific substitution from a vcf file
written by sambioinfo2018 •
-
Qual score in VCF file
written by swatipuraanik •
-
Checking kinship coefficients and relationships and comparing genotyping data to exomes
written by DG
-
Filtering Vcf File For Fixed Substitutions
written by Rubal7
-
Vcftools --Freq
written by kai.clarkson •
What are "homeologous" SNPs? Do you mean "homologous", maybe? Please edit your post and add a link to the article you refer to.
I guess it's this one: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0159437
Yes, the same article, thanks