Question: Variation Count Based On Chromosome
0
gravatar for win
5.3 years ago by
win810
India
win810 wrote:

I have a VCF file and i want the count of variations per chromosome i.e. for each chromosome how many variations found. i am aware that the command lc - w <filename> will give the count of total lines in the VCF but how could i indicate the chromosome number such as chr1, chr2 etc...

help much appreciated.

vcf • 2.2k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 5.3 years ago by win810
6
gravatar for Pierre Lindenbaum
5.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:
 grep -v -E '^#'  your.vcf | cut -f 1 | sort | uniq -c
ADD COMMENTlink written 5.3 years ago by Pierre Lindenbaum118k
0
gravatar for Vivek
5.3 years ago by
Vivek2.2k
Denmark
Vivek2.2k wrote:
awk '! /\#/' varaints.vcf | awk '{print $1}' | sort | uniq -c
ADD COMMENTlink written 5.3 years ago by Vivek2.2k
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