Detailed explanation of the use of vcfFilter_DP_Freq.pl file

[mario2437]

Hello. Thank you for developing this great tool!

I tried to use "vcfFilter_DP_Freq.pl" commend on my system, yet I cannot find which format I need to adhere for each parameters.
From the guideline, I can see the following explanations.

The DP and FREQ values from the output vcf file can be obtained using:
perl vcfFilter_DP_Freq.pl --input=outVCF.vcf --list=sampleList.txt --DP=30 --AD=5 --FREQ=25

I believe it would be very helpful if the users have access to the example "outVCF.vcf" and "sampleList.txt" files.
Also, I have multiple vcf files to be analyzed. How do I put them in the --input part? at once?

Thank you again !

[vincegur]

I had the same issue.
The script did not recognize the files given as arguments.
Changing line 33 to:
open(fileIn, "<".$options{'input'}) || die "Err fileIn:$!\n";
made the trick for me...

As far as I understand, "sampleList.txt" is just used to name the samples from a multi-sample VCF file.

Hope this helps!

[ebartom]

I, too, had this issue.

VCF is a very flexible file format, with different values in different fields depending on the tool (and parameters) used to generate the VCF file.

Can you include the parameters (and software version) you used for VarScan to generate a VCF file from a BAM file? Presumably the resulting VCF file would be correctly read by vcfFilter_DP_Freq.pl file to generate the DP and FREQ files that are necessary inputs to CeL-ID.