Extracting information from my VCF file

Question

[realtreeecat]

Chrom Pos ID  REF ALT     QUAL    FILTER  INFO    FORMAT  EPISL_12878 [other samples...]
NC_045512.2 2   NC_045512.2_2_T_C   T   C   .   PASS ANN=C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-264T> GT   .   .   .   .   .   1   .   .   .

I'm new to using VCF data and have merged all my VCF files for my samples, resulting in a combined VCF file. It contains mutation information represented as '.' and '1'. How can I extract mutations, (for e.g.,all mutation in 'ORF1ab' gene) from this file?

If merging VCF files isn't recommended, how can I efficiently extract information from individual VCF files, considering I have over 5 thousand samples? Thank you.

[Ram]

If merging VCF files isn't recommended

Where did you get that idea from?

Please read the bcftools manual for a multitude of ways to work with VCF files.

[Pierre Lindenbaum]

bcftools view --regions bed_for_your_gene.bed indexed.vcf.gz

[bioruffo]

Just a note - if multiallelic sites are not split in your VCF, then you don't have only "." and "1"; you can have 2, 3... referring to the second, third etc. alt alleles.