Mutect2 GVCF

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• September 26, 2024 02:01

I'm trying to get gvcf files with Mutect2, but apparently -ERC option is not available anymore.. Is there any way I can get gvcf files?
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/kds/.conda/envs/py311/share/gatk4-4.0.5.1-0/gatk-package-4.0.5.1-local.jar Mutect2 -R /data/ref/human/human_g1k_v37.fasta -I /data/med3_data/DATA3/gh/DB15_kidneywholebulk_x100x300/DB15_RKLK_comp/Only_Dragen_RKLK/15_LK_91.s.md.ir.bam -tumor 15_LK-91 -L /data/temp_intern/intern/choi/all_py.code/BED_interval2.bed -ERC GVCF -O 15_LK_91.vcf
USAGE: Mutect2 [arguments]

Call somatic SNVs and indels via local assembly of haplotypes
Version:4.0.5.1

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A USER ERROR has occurred: E is not a recognized option

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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
sorry.

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  Gökalp Çelik

  • September 27, 2024 18:06

  Hi

  The option is still there as of version 4.6.0.0. 

  --emit-ref-confidence,-ERC <ReferenceConfidenceMode>
                                Mode for emitting reference confidence scores (For Mutect2, this is a BETA feature) 
                                Default value: NONE. Possible values: {NONE, BP_RESOLUTION, GVCF}

  Can you try using the latest version? Also can you check your command line parameters to see if you have a faulty whitespace where you have -ERC parameter?

  Regards. 

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