Error HaplotypeCaller from alternate contigs tutorial
Answered
Hi! I am trying to follow this tutorial: https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-reference-with-alternate-contigs-like-GRCH38 and I got the error below:
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:
gatk-4.1.9.0
b) Exact command used:
gatk HaplotypeCaller -R refhg38P -I input.bam -O output.haplo.g.vcf -ERC GVCF --emitDroppedReads -bamout output.haplo.hc.bam
c) Entire error log:
A USER ERROR has occurred: emitDroppedReads is not a recognized option
My questions are: do I need to add this emitDroppedReads in the command for GATK4? I know that the tutorial is for GATK3 and has not yet been adapted for GATK4 and I am unsure if emitDroppedReads is automatically done by GATK4 HaplotypeCaller since I do not see it in the Tool Docs. If not, how do I add it in? Is it no longer recommended by GATK?
Thank you in advance!
-
Official comment
Linda Do Unfortunately it doesn't look like the option has been ported to GATK4 yet, there has already been a issue ticket created, however: https://github.com/broadinstitute/gatk/issues/5010
You can follow along there, though it looks like it is not the highest priority for the team. You can look through the other HaplotypeCaller current options in the tool docs: https://gatk.broadinstitute.org/hc/en-us/articles/360056969012-HaplotypeCaller
Comment actions -
Hi Linda Do,
I am going to move your post into our Community Discussions -> Documentation Questions topic, as the Other topic is for reporting bugs and issues with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
Best,
Genevieve
-
Thank you for answering!
So should I use the GATK3 version of HaplotypeCaller for this step? Are the HaplotypeCaller from GATK3 and HaplotypeCaller from GATK4 very different? Are there benefits to using HaplotypeCaller from GATK4 over HaplotypeCaller from GATK3?
Thank you in advance!
-
Unfortunately, I don't have a solid answer about this since the tutorial has not been updated to GATK4. I am not sure what will be the difference from not using the emitDroppedReads option.
HaplotypeCaller in GATK4 has many improvements and benefits, you can read about all the changes in our release notes: https://github.com/broadinstitute/gatk/releases
If you want to search our old legacy forum for information regarding this topic, here is the link: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/
Please sign in to leave a comment.
4 comments