Hi,
I need to extract chr 1-22 from SNP array data which also contains mtDNA and Y SNP data. Plink does it chromosome by chromosome and in this case I need to extract one chromosome by another and then join it, but I need something by which I can do it in one command.
Alternatively, the way to remove mt and Y SNPs from the main file would also work equally.
Please help if somebody can write the commands.
Thanks
•
written
by
User 0422 •
awk '{ if ($1 == 1 || $1 == 22) print $2 }' file.bim > snp.txt
plink --bfile file --extract snp.txt --make-bed --out newfile
this gives me only 1 and 22 numbers of chromosomes while I need 1 to 22! thanks
Sorry, I misunderstood your question.
awk '{ if ($1 >= 1 && $1 <= 22) print $2 }' file.bim > snp.txt
great! many thanks
thx Baboune. It helped me too.
Assuming it's a bed file, or some other file that has the chromosome name in the first column, it's as simple as doing
perl -ne 'print $_ if /^chr[12]?[0-9]/' yourfile >outfile
As Aaron said, it's difficult to tell you about the others without a sample of the file format.
You really should read up on regular expressions, and the use of grep, awk, sed, or perl to do pattern matching.
Log in to answer this question.
Providing an example of the contents of your file will likely lead to a quick answer.