152 results in 0.0039 seconds.
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Introductory NGS data analysis & variant calling workshops (online and in-person, early 2026)
For those looking for a structured introduction to NGS data analysis and DNA variant calling, we're running the same introductory workshop in two for...
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Read depth extraction
Hello. I wanted to extract the read depth information from my vcf file. Can anyone share their her/his experience in doing this. My vcf format is like... -
Insertions follow reference in vcf file
Hi,
I'm working with gvcf files, containing also non-variant positions. I have noticed some insertions that I'm not able to correctly interpret... -
Introducing Genozip - genomic file compressor
I would like to introduce a compression software package I developed: Genozip (www.genozip.com).
It is a tool with the primary objective... -
PacBio software vcf and consensus fasta do not agree
I'm using PacBio's "variantCaller" tool (v6) to call variants on some older RSII subread data I aligned with blasr. The reference is 14845... -
Genotype call incorrect in freebayes output?
So I ran freebayes 1.3.1 with all the default parameters on dog dna samples. I am getting this result for one of the samples (although it seems to be...Last edited by najoshi; 07-08-2020, 03:15 AM. -
VCF to RQTL format for genetic mapping?
Hi everyone,
I am new to this forum and bioinformatic methods. I have whole genome resequencing data for 180 haploid individual from same mother... -
How to regenerate an index file for a gzipped vcf file?
I have a large vcf file with genomic data (330 GB) and an index file that accompanies it. I ran the command:
bcftools view -f PASS... -
vcftools and bcftools disagree
Hello,
I'm trying to impute my data using HRC (sanger server). For that I validated and annotated my vcf using GATK and then prepared... -
bcftools output type not recognized
I am trying to find a single SNP on a bunch of dog genomes in a compressed vcf file (vcf.gz) and I have been using bcftools to do so. I posted before... -
Accessing Genomic data in a large vcf.gz file
Hello all, I am very new to bioinformatics; I'm a high school intern. I have a .vcf.gz file that is 332 GB. It contains the whole genomes of around 800... -
Tools to check consistency between VCF genotypes & pedigree-stated sex/relationship?
X-post from Biostars.
We're currently trying to do identity checks on targeted genome sequencing data from ~15K samples. Our target panel... -
some variants disappear after bcftools norm
Hello,
I noticed that when performing left-normalization on my vcf file (as suggested by Annovar at http://annovar.openbioinformatics.... -
bbmap callvariants.sh multisample vcf format, wrong number of fields
Trying to use BBMap callvariants on multiple samples. The resulting VCF does not have the sample names and yields an error with any vcf tools:
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Adding a fake genotype column to a vcf file
Hello all!
I need to add a fake genotype column to my vcf files produced with lofreq in order to use them with vcf tools for specific analyses....
