LeftAlignAndTrimVariants removes header tags

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registered_user

• September 22, 2020 08:03

I noticed that LeftAlignAndTrimVariants (GATK 4.1.8.1) keeps only the first entry of normal- and tumor sample header tags in VCF files. This is unexpected and unwanted behavior. Trimming should not remove any of these tags.

##normal_sample=n1
##normal_sample=n2
##tumor_sample=t1
##tumor_sample=t2

becomes

##normal_sample=n1
##tumor_sample=t1

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• 

  Genevieve Brandt (she/her)

  • September 22, 2020 20:02

  registered_user could you please submit your command and complete stack trace?

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