1000 genome data

Question

[Peerzada]

I want to know that How I can get the genomic sequence of my gene of interest that is 'aqp 1' for 1000 individuals from the vcf data that is present in the 1000 genome project .I know the chromosome location of the aqp1 is chr 7 from 30911853-30925516.Kindly tell about the commands so that I can process vcf file from 1000 genomes to get my gene of interest .

[GenoMax]

See:

https://www.internationalgenome.org/faq/how-can-i-get-all-variants-in-a-particular-gene/
https://www.internationalgenome.org/faq/how-can-i-get-gene-sequences-for-individuals/

Answer 1

[Pierre Lindenbaum]

 bcftools view "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr7.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz" "7:30911853-30925516"

[Peerzada]

After running command I got output as a variant file with 0l0 and 0l1 for some positions of all individuals . How can I get the sequence of whole gene with those variants incorporated and find the exonic and intronic region of the gene .