SnpSift case control command for multiple samples

Question

[kumari.indu31]

We are trying to write a script which can analyse multiple samples for SnpSift CaseControl. There is "+" symbol in the command to represent the no. of samples. How to define this option of the command in the script. Here is the script, we are trying to run, but it is not working.

!/bin/bash

for f1 in *vcf do java -jar SnpSift.jar caseControl "$f1+" $f1 > $f1_CC.vcf done

Please help with this.

[e.rempel]

Just a few remarks:

• if you use for loop in one line, the syntax should be different and contain semicolons. Otherwise, you could use indentations.
• if I am not mistaken, the usual input for caseControl is a vcf file with multiple samples in it (meaning multiple sample columns in the vcf file). In this case, the symbols +, -, 0 specify whether the case is cancer, control, or neutral.

[kumari.indu31]

My question is regarding how can I define no. of samples in the command in script so that there is no need to add "+" symbol manually.

[Arup Ghosh]

You can't run caseControl without a multi sample vcf.