I have some very large WGS BCF files and I would to extract just the first 8 columns, thus reducing to just a 'sites-only' VCF/BCF. Does BCFTOOLS have a canned option for doing it? I know I can do this: query -f "%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO\n" but I'm finding that that is quite slow (>24hrs for some files...

When you write the enhanced volcano code; using this as an example... EnhancedVolcano(filtered_mutant1, lab = filtered_mutant1$gene, x = 'avg_log2FC', y = 'p_val', xlab = bquote(~Log[2]~ 'fold change'), title = "Cluster 1: BGH vs WT", pCutoff = 0.05, ...

Hello! I am an absolute beginner to python, attempting to learn it for genomics purposes, and I’ve been self-teaching through an online course. From the course, and many, many other examples of the internet I have made the below mess of a code. It works perfectly until the has_start_codon part. I have been working through Visual Studio Code’s python...

Hello, I'm annotating a vcf file using ensembl vep and gnomad v4 vcf file: vep --cache --offline --species homo_sapiens --assembly GRCh38 \ --input_file input.vcf \ --custom gnomad.vcf.bgz,gnomADg,vcf,exact,0,AF because the `gnomad.vcf.bgz` file contains all variants including low quality ones (specified in the FILTER...

I probably got some of the vocabulary wrong. I thought that "Dom HOR2932 HOR3036 HOR3726 KWSBambina Rec S42IL_124" were representing my genotpyes. Anyway, what i want to remove from my file is all Variants which "belong" to KWSBambina. Is that possible? How do I identify, which of the Variants belong to Bambina?

It's featureCount**s**, not featureCount. I've edited your post and fixed all mentions of featureCounts.