GATK4.3.0

Question

[wonde2000]

Hi all,

I am working with GATK version 4.3.0. I am a bit confused which code can I used for VQSR and ApplyVQSR.

I found the code for ApplyVQSR on https://gatk.broadinstitute.org/hc/en-us/articles/9570419503259-ApplyVQSR while for the first step (VQSR) I did not find the code for the version am using it.

In addition, even though the version of GATK is not indicated, I found different code updated in Jun, 2023. https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering

Here in the updated version, for example the reference sequence is not available in the command line. Is there any one who have had solution for such difficulties

[dthorbur]

Why don't you just follow the example code in the ApplyVQSR documentation for the version you have? Whilst I agree the blog post is confusing since the most recent version requires the -R parameter, what's stopping you from seeing if you get an error following the code on the docs page for ApplyVQSR (v4.3.0)?

I don't understand your point about finding the code for the version you are using. The docs page you linked is for v4.3.0.

[wonde2000]

You are right! It is clear for ApplyVQSR. However, I couldn't find the command clearly indicated for the first part of VQSR (i.e. VariantRecalibrator) for version GATK 4.3.0. Thank you!

[dthorbur]

This one?