Shell Programming and Scripting

 If $11 is not equal to "unknown", then in a new text file $4, $11, $7, $13

 awk 'BEGIN{OFS=FS=","}NR==FNR{a[ $11 <> "unknown"];next} in a{print $4,$11,$7,$13}' test.txt > newfile.txt

awk 'BEGIN{OFS=FS=","}$11 != "unknown"{print $4,$11,$7,$13}' test.txt > newfile.txt

 awk 'BEGIN{OFS=FS=","}$11 != "unknown"{print $4,$3,$7,$13}' file.txt > newfile.txt

 The output doesn't look correct and I'm not sure why.  If $11 = "unknown" then that entire record doesn't need to be copied to the newfile.txt 

For example, row 24 $11 is not unknown, so the record is copied to newfile.txt this way:

A_16_P39089234, chr10:76765556-76765615, KAT6B, 0.9337

In row 2 $11 equals "unknown", so it is not copied to newfile.txt.  The starting spreadsheet is excel so there is a header row in it that can be removed.

 awk '$11 != "Unknown"  && $11 != "" {print $4,$3,$7,$13}' FS="\t" OFS="," file.txt