Hello Bastien, My vcf file does't contain any chr word as a result your command is not working.
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How can I get 31 chromosome from vcf file?
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.
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1 answer
grep '^chr' variants.vcf | cut -f 1 | sort | uniq -c
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So, you need a convertion table from your chromosome names (NC_005044.2, NC_030808.1...) to standard chromosome names (chr1, chr2...)
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How can I create a conversion table?
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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?
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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.
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What does this exactly mean? Are you concerned that there are > 31 entries that look like chromosomes?
yes, How can I differentiate them. There are two tags "NC" and "NW" . What does "NW" mean.
NCare fully assembled chromosomes.NWare scaffolds/rcontigs that would still be part of the genome. They would haveNNNNwhere there is missing sequence. You can find a full listing here.