How can I get 31 chromosome from vcf file?

Question

[Mbillah]

I have a vcf file. When I run this command grep -v -E '^#' variants.vcf | cut -f 1 | sort | uniq -c I got 6835 line. But my chromosome number is not greater than 31. Is there any way to specify 31 chromosome form this 6835 line. The lines are look like:

 NC_005044.2
 NC_030808.1
 NC_030809.1
 NC_030810.1
 NC_030811.1
 NC_030812.1
 NC_030813.1

Thank you.

[GenoMax]

Is there any way to specify 31 chromosome form this 6835 line.

What does this exactly mean? Are you concerned that there are > 31 entries that look like chromosomes?

[Mbillah]

yes, How can I differentiate them. There are two tags "NC" and "NW" . What does "NW" mean.

[GenoMax]

NC are fully assembled chromosomes. NW are scaffolds/rcontigs that would still be part of the genome. They would have NNNN where there is missing sequence. You can find a full listing here.

Answer 1

[Bastien Hervé]

grep '^chr' variants.vcf | cut -f 1 | sort | uniq -c

[Mbillah]

Hello Bastien, My vcf file does't contain any chr word as a result your command is not working.

[Bastien Hervé]

So, you need a convertion table from your chromosome names (NC_005044.2, NC_030808.1...) to standard chromosome names (chr1, chr2...)

[Mbillah]

How can I create a conversion table?

[Bastien Hervé]

In your post you missed some essential informations, as the species you are working on, seems like to be Capra Hircus. Here, you can find the conversion table for your chromosomes

[Mbillah]

Yes my species is Capra Hircus. Can you tell me what does "NW" mean? and How can I find start and End position of each chromosome?

[GenoMax]

You can find the assembly/annotation report for Capara here. Scroll down the page and click on Assembly statistics tab to get the start-stop for each chromosome. Note: There are two goat assemblies. One linked here is for ARS1.