Can I know the progress of Haplotypecaller?

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JE S

• April 06, 2022 07:19

REQUIRED 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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  Genevieve Brandt (she/her)

  • April 06, 2022 20:39

  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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  Genevieve Brandt (she/her)

  • April 13, 2022 03:06

  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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