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Build the SNP recalibration model error
I am trying to build the SNP recalibration model by running the following GATK command:
./gatk-22.214.171.124/gatk VariantRecalibrator \
-R human_g1k_v37_decoy.fasta \
-input /mergedFiles.vcf \
--resource hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \
--resource omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf \
--resource 1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.vcf \
--resource dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_135.b37.vcf \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff \
-mode SNP \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
--recalFile recalibrate_SNP.recal \
-tranchesFile output.tranches \
But I am getting following error.
A USER ERROR has occurred: Invalid argument 'hapmap_3.3.b37.sites.vcf'.
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
I have used the human_g1k_v37_decoy.fasta for alignment therefore, using the same for recalibration. I would like to convert raw variants to ready to analysis variant by applying filtration,and annotation. Please let me know if you have any direction for best practice approach.