Finding Mutations In A Gene From 69 Genomes

Question

[Pappu]

So first I downloaded files like vcfBeta-NA10851-200-37-ASM.vcf.bz2 from the complete genomics website. Then I had to convert it to gz and index by tabix for fast extraction of variation in chromosome positions. I realized that I have to do the same for 69 genomes which is tiresome.

Then I downloaded CompletePublicGenomes69genomesall_testvariants.tsv.bz2. After unzipping, the file size is 7.2 GB. Let me know how can I work with this file since the format is unknown to me. Thank you.

Answer 1

[Sean Davis]

This is a tab-separated-value format file. There are many tools for working with .tsv files, but some (Excel is a prime example) will probably not work with such a file unless you split it into smaller pieces. A scripting language or the linux/unix command line utilities like grep and awk are probably necessary. For your problem, I would consider using grep to pull out lines in the original file that contain variants in your gene of interest. Then, use this subset of the file in Excel.

[Pappu]

Thank you for your suggestion. I actually tried sed which seemed to be too slow for such huge files. I am worndering if it would be possible to convert it to vcf and index by tabix for fastest access to chromosome regions.

[Sean Davis]

You do not need to convert to VCF. Tabix will happily index any sorted, bgzipped file given the correct arguments for chromosome, start, and end columns.