No headers found in VCF

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Qing Zhang

• January 26, 2021 17:42

Hi GATK Team,

I am working on a pipeline that has to write a minimal VCF to be funcotated. However, when I run `Funcotator` or `ValidateVariants`, I got the following error:

```

htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file

```

Attached a part of mt VCF file (where "#CHROM" does appear):

```

##normal_sample=759d9ab7-8584-45c6-8882-6b64697edfbf
##tumor_sample=e94bafbc-cfcc-4b38-ab40-c87f2c091466
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 759d9ab7-8584-45c6-8882-6b64697edfbf e94bafbc-cfcc-4b38-ab40-c87f2c091466
chr1 946293 . G T . PASS SOMATIC AD 79,0 105,20

```

Just in case there is confusion between whitespace vs tabs, I attached the file with the post.https://drive.google.com/file/d/1ckc_6qTAtepVJM4l9E7w6z_y1rUlf0fq/view?usp=sharing 

 

Thanks!

 

0

• 

  Qing Zhang

  • January 26, 2021 18:15

  Sorry I found the problem! I was not populating the headers correctly - I missed `##` in some lines. Thanks!

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• 

  Genevieve Brandt (she/her)

  • January 27, 2021 19:28

  Hi Qing Zhang, thank you for the update and posting your solution! I am sure it will be helpful for members of the GATK community in the future.

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