A simple SNP calling pipeline
Filtering of VCF Files
Filtering vcf using bcftools filter-Expression Question · Issue #1224 · samtools/bcftools · GitHub
Subsetting with `bcftools filter file1.vcf.gz -r chr#` fails for majority of chromosomes · Issue #774 · samtools/bcftools · GitHub
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
bcftools filter -e 'GT="het"' recognize GT 2/2 as heterozygous · Issue #1268 · samtools/bcftools · GitHub
bcftools/filter.h at develop · samtools/bcftools · GitHub
Mapping Summary and Extension
Calling Variants using WES data and samtools + bcftools – Dami's blog full of codes
filter by major DP4 · Issue #1064 · samtools/bcftools · GitHub
Filtering of VCF Files
A Map of 3′ DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes
Comparing -min-DP in vcftools with filter -i 'FORMAT/DP>10' in bcftools · Issue #1384 · samtools/bcftools · GitHub
bcftools filter on per-sample FORMAT fields · Issue #1010 · samtools/ bcftools · GitHub
SNP calling and filtering pipelines used in our experiments. (A) In... | Download Scientific Diagram
Q: filter according to a file containing variant IDs · Issue #776 · samtools/bcftools · GitHub
bcftools filter -e 'GT="het"' recognize GT 2/2 as heterozygous · Issue #1268 · samtools/bcftools · GitHub
CallSNPs.py - wiki
Protocol for unbiased, consolidated variant calling from whole exome sequencing data - ScienceDirect
The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species | Scientific Reports
Filter on FORMAT fields · Issue #51 · samtools/bcftools · GitHub
Command Line - Andersen Lab Dry Guide
bcftools view | bcftools tutorial on how to count the number of snps and indels in a vcf file - YouTube
bcftools view | bcftools tutorial on how to count the number of snps and indels in a vcf file - YouTube
