How do I get the output of --bam-out from an exsiting vcf with HaplotypeCaller

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shimijuan

• March 14, 2024 02:06
• Edited

I have a VCF file and I want to obtain the assembled haplotypes through --linked-de-bruijn-graph --bam-out without rerunning the HaplotypeCaller to generate the VCF again. Does the current version of GATK have this functionality?

REQUIRED for all errors and issues:

a) GATK version used:
b) Exact command used:
c) Entire program log:

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  Gökalp Çelik

  • March 14, 2024 02:58

  Hi shimijuan

  --bam-out must be activated during the time when variant calling is done therefore you cannot go back from a VCF to assembled haplotypes. Unfortunately you need to run HaplotypeCaller again for those regions that you have a variant of interest. 

  I hope this helps. 

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