7. Variant calling — Genomics Tutorial 2020.2.0 documentation
Command Line - Andersen Lab Dry Guide
A simple SNP calling pipeline
BCFtools filter - Issue with DP and basic question · Issue #1209 · samtools/ bcftools · GitHub
Calling Variants using WES data and samtools + bcftools – Dami's blog full of codes
Filtering vcf using bcftools filter-Expression Question · Issue #1224 · samtools/bcftools · GitHub
First steps in genomic data analysis - Evolution and Genomics
PDF) How to extract and filter SNP data from the genotyping-by- sequencing (GBS) data in vcf format using bcftools
bcftools not recognizing 'F_MISSING' in filter · Issue #704 · samtools/ bcftools · GitHub
Bioinformatics and other bits - Run bcftools mpileup in parallel with Python
5. Variant calling and visualization — Physalia Paleogenomics 0.1.0 documentation
bcftools view | bcftools tutorial on how to count the number of snps and indels in a vcf file - YouTube
Filtering of VCF Files
A Map of 3′ DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes
Variant Calling with BCFTOOLS | Galaxy Tutorial - YouTube
bcftools/filter.h at develop · samtools/bcftools · GitHub
bcftools view | bcftools tutorial on how to count the number of snps and indels in a vcf file - YouTube
bcftools filter -e 'GT="het"' recognize GT 2/2 as heterozygous · Issue #1268 · samtools/bcftools · GitHub
Filtering of VCF Files
Filtering vcf using bcftools filter-Expression Question · Issue #1224 · samtools/bcftools · GitHub
IJMS | Free Full-Text | Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing
CallSNPs.py - wiki
Filtering of VCF Files
Possible to annotate the FILTER from an annotation VCF file, as an INFO/TAG in the target? · Issue #1187 · samtools/bcftools · GitHub
The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species | Scientific Reports
