Can I know the progress of Haplotypecaller?
AnsweredREQUIRED for all errors and issues:
a) GATK version used: 4.1.3.0
b) Exact command used: gatk HaplotypeCaller -I alignment_rmdup.bam -O variants.g.vcf.gz -R genomic.fna --max-alleles 2 --emit-ref-confidence GVCF
c) Entire program log:
I am new to GATK. When analyzing resequencing data using Haplotypecaller, can I check the time remaining or the progress of the analysis?
thanks for the reply
See forum topic details at forum guidelines page: https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines
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Hi JE S,
I am going to move your post into our Community Discussions -> General Discussion 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
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Hi JE S,
HaplotypeCaller does not estimate the time remaining, but you can view the progress in the progress meter, which will appear in the standard output by the tool.
Let me know if you have any further questions.
Best,
Genevieve
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