If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Why the option -env did not exclude all the non-variant sites ?


I use SelectVariants to remove some sample out of may initial data. In doing that, I ended up having some sites for which there is no variant as the variation was removed with samples that had been removed...
However, when I add the option -env (--excludeNonVariants) in order to remove all the sites where there is no variation between samples. I still have sites where there is no variation between samples, but different from the reference, in the vcf file.

Here is my command:

java -Xmx4G -jar /path/to/GenomeAnalysisTK.jar -T SelectVariants -R /path/to/ref.fa -V starting_vcf_file.vcf -env -o results_vcf_file.fa

I expect the results vcf file to contain only sites with variation between the samples. However I still have sites such as

scaffold1 25003 . T C 40226.42 PASS AC=14;AF=1.00;AN=14;DP=866;ExcessHet=0.2482;FS=0.000;MQ=60.06;QD=31.72;SOR=1.046 GT:AD:DP:GQ:PL 1:0,54:54:99:2427,0 1:0,69:69:99:3089,0 1:0,83:83:99:3807,0 1:0,35:35:99:1530,0 1:0,40:40:99:1842,0 1:0,31:31:99:1405,0 1:0,65:65:99:2899,0 1:0,43:43:99:1935,0 1:0,55:55:99:2464,0 1:0,64:64:99:2900,0 1:0,86:86:99:3850,0 1:0,91:91:99:4182,0 1:0,84:84:99:3817,0 1:0,66:66:99:3029,0

As you can see, there is no variation between the samples ! Does GATK consider all sites where all samples have the alternative allels as variants ???
If this is the case, how can exclude these sites ?

Thank you very much in advance.

Best Answer


Sign In or Register to comment.