Extract Mitochondrial Genome Sequence from 1000 Genomes Data

Question

[ammarsabir15]

Is it possible to extract mitochondrial genome sequence from whole genome sequence data available in 1000 genomes?

If yes then how is it possible? I mean can we do it using a script or is there any online data extraction tool available for this purpose. ?

[Fernanda]

Hi, did you find out?

Answer 1

[GenoMax]

Sequence file is available here. Answer originally provided in this thread: 1000 genomes project mitochondrial DNA sequences

[ammarsabir15]

@genomx your answer provides the way to get fasta sequence but I want to extract sequence in fastq format from whole genome sequence.

[GenoMax]

1000 genomes data is available at this FTP link. You may be able to use an API to get what you need.

[ammarsabir15]

I am aware of ftp link for 1000 genome data, for the API link there are mostly tools related to data analysis and I doesn't found a tool or documentation to solve my problem. Is there any simple way to extract mitochondrial genome in fastq format from whole genome sequence of an individual from 1000G data? Even if this can be done using a script?