Gonna write a paper on this. PLEASE DON'T USE VCFTOOLS TO CALCULATE π. It is a random number generator, as the software assumes all bp that aren't SNPs are invariant (i.e. ignores missing data). This is especially bad in plant genomes, with abundant TEs where you can't map reads.
February 1, 2024 at 5:19 PM
Gonna write a paper on this. PLEASE DON'T USE VCFTOOLS TO CALCULATE π. It is a random number generator, as the software assumes all bp that aren't SNPs are invariant (i.e. ignores missing data). This is especially bad in plant genomes, with abundant TEs where you can't map reads.
I thought that’s what vcftools was doing
April 16, 2025 at 12:28 AM
I thought that’s what vcftools was doing
With @benoitevol.bsky.social, we developed our own strategy to properly estimate π (e.g. doi.org/10.1016/j.cu...) and I extended it to variable ploidy (doi.org/10.1093/gene...). But it's clearly not as user-friendly & computationally efficient as pixy for similar results
➡️Use pixy, forget VCFtools!😉
➡️Use pixy, forget VCFtools!😉
July 31, 2026 at 7:53 AM
With @benoitevol.bsky.social, we developed our own strategy to properly estimate π (e.g. doi.org/10.1016/j.cu...) and I extended it to variable ploidy (doi.org/10.1093/gene...). But it's clearly not as user-friendly & computationally efficient as pixy for similar results
➡️Use pixy, forget VCFtools!😉
➡️Use pixy, forget VCFtools!😉
Stop estimating pi with vcftools in 2024
October 24, 2024 at 10:00 PM
Stop estimating pi with vcftools in 2024
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #reproducibility
www.biorxiv.org
June 8, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #reproducibility
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
www.biorxiv.org
June 13, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
www.biorxiv.org
October 7, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
www.biorxiv.org
September 16, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
www.biorxiv.org
July 30, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
www.biorxiv.org
June 26, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
www.biorxiv.org
July 27, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
www.biorxiv.org
July 22, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
www.biorxiv.org
August 15, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
www.biorxiv.org
August 15, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
EGP1K: Whole-Genome Sequencing of 1,024 Egyptians Characterizes Population Structure and Genetic Diversity
www.biorxiv.org
April 10, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
Genomic Prediction Enables Provenance-Aware Selection in Sessile Oak (Quercus petraea) using Foliar Physiological Traits
www.biorxiv.org
April 6, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
FastGxC: Fast and Powerful Context-Specific eQTL Mapping in Bulk and Single-Cell Data
www.biorxiv.org
March 31, 2025 at 12:04 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
How social and economic policies have affected the genome of mezcal agaves: the contrasting stories of Bacanora and Espadín
www.biorxiv.org
May 6, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
Genome-wide characterization of upper Fraser River sockeye salmon identifies a region of major differentiation between run timing groups in the Stuart River Watershed
www.biorxiv.org
June 11, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
The populations VCF import function is designed only for variant sites. You could re-export the VCF from populations with the alt population map. If you want to keep your filtering, you can use the loci that were not filtered by vcftools to make a whitelist to feed into populations at the same time
March 27, 2024 at 3:36 AM
The populations VCF import function is designed only for variant sites. You could re-export the VCF from populations with the alt population map. If you want to keep your filtering, you can use the loci that were not filtered by vcftools to make a whitelist to feed into populations at the same time
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
www.biorxiv.org
August 31, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
PopGenAgent: An Agent-Mediated Workflow for Population Genetics Analyses
www.biorxiv.org
August 15, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used VCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
Intensive brainstorming session on #vcftools at @TransmitScience #NGS training session #IamTransmittingScience
November 25, 2024 at 4:09 PM
Intensive brainstorming session on #vcftools at @TransmitScience #NGS training session #IamTransmittingScience
Okay… I am back at this… and I have a question:
I made an all-sites VCF using pppulations w/ all individuals as one pop, no probs there. Split out variant and invariant sites, did some VCFtools filtering, and recombined them. Then running populations again, but w/ each pop separated on popmap (1/2)
I made an all-sites VCF using pppulations w/ all individuals as one pop, no probs there. Split out variant and invariant sites, did some VCFtools filtering, and recombined them. Then running populations again, but w/ each pop separated on popmap (1/2)
March 27, 2024 at 1:30 AM
Okay… I am back at this… and I have a question:
I made an all-sites VCF using pppulations w/ all individuals as one pop, no probs there. Split out variant and invariant sites, did some VCFtools filtering, and recombined them. Then running populations again, but w/ each pop separated on popmap (1/2)
I made an all-sites VCF using pppulations w/ all individuals as one pop, no probs there. Split out variant and invariant sites, did some VCFtools filtering, and recombined them. Then running populations again, but w/ each pop separated on popmap (1/2)