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:
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!
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