problem with output from combinegvcf gatk 4.1.3

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flaviarogerio

• April 12, 2020 13:23

Hi gatk users,

I'm using gatk/4.1.3.0

I need to combine three vcf files previously created by haplotypecaller

I'm using the command:

gatk CombineGVCFs -R CTRU02_final_assembly.fasta --variant C1_max_missing.recode.vcf --variant C2_max_missing.recode.vcf --variant C3.vcf -O cohort.g.vcf

However, the output created lacks the ALT in the header field, showing just the <NON_REF> in the samples. 

 Is there something missing in this command?

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• 

  Bhanu Gandham

  • April 12, 2020 20:09

  Take a look at these docs :https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format

  https://gatk.broadinstitute.org/hc/en-us/articles/360035531532-HaplotypeCaller-Reference-Confidence-Model-GVCF-mode-

  https://gatk.broadinstitute.org/hc/en-us/articles/360035890411-Calling-variants-on-cohorts-of-samples-using-the-HaplotypeCaller-in-GVCF-mode

  https://gatk.broadinstitute.org/hc/en-us/articles/360035889971--How-to-Consolidate-GVCFs-for-joint-calling-with-GenotypeGVCFs

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