HaplotypeCaller -ERC GVCF -variant_index_type LINEAR
Hello, I am following the workflow for joint genotyping here: https://gatk.broadinstitute.org/hc/en-us/articles/360035890411-Calling-variants-on-cohorts-of-samples-using-the-HaplotypeCaller-in-GVCF-mode
I am using gatk version 4.0 , I am facing this error in HaplotypeCaller:
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A USER ERROR has occurred: variant_index_type is not a recognized option
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gatk HaplotypeCaller \
--reference ~/hs37d5.fa \
--input ~/GATK/test_joint_genotype/$id”Al_sort_md_sN_RG_bqsr.bam” \
--output ~/GATK/test_joint_genotype/$id”Al_sort_md_sN_RG_bqsr_HCT.g.vcf” \
-ERC GVCF \
--variant_index_type LINEAR \
--variant_index_parameter 128000
I tried again this time changing the parameter from --variant_index_type LINEAR
to -variant_index_type LINEAR and I got this error:
***********************************************************************
A USER ERROR has occurred: v is not a recognized option
***********************************************************************
gatk HaplotypeCaller \
--reference ~/hs37d5.fa \
--input ~/GATK/test_joint_genotype/$id”Al_sort_md_sN_RG_bqsr.bam” \
--output ~/GATK/test_joint_genotype/$id”Al_sort_md_sN_RG_bqsr_HCT.g.vcf” \
-ERC GVCF \
-variant_index_type LINEAR \
--variant_index_parameter 128000
I would appreciate help on how to solve this. Thank you in advance.
-
Hi Matilde
You are using a very old version of GATK which we do not support anymore. Please upgrade to the latest version of GATK v 4.1.9.0. The latest version of GATK does not require "-variant_index_type" argument anymore. That was a temporary workaround for an issue with index compression in a very old version of GATK.
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