Mutect2 output vcf FORMAT not accepted

[zacshi]

When fed with vcf files from GATK4(version gatk-4.0.1.2) Mutect2, I got error message:

2018-04-26 12:37:19 - pcgr-validate-input - ERROR - According to the VCF specification, the VCF file (/workdir/input_vcf/AE188.mutect2.vcf.gz) is NOT valid:
ERROR: Line 119: Format is not a colon-separated list of alphanumeric strings

However the lines before line 119 are all the same as line 119
The FORMAT in Mutect2 vcf in line 119 looks the following,
GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB

AE188.mutect2.vcf.gz

Is that the underscore that is not accepted?

[sigven]

Hi,

Yes, that’s my experience previously. Underscores are not permitted in the FORMAT columns. You can disable the strict VCF-validator in the config file (PCGR is either way ignoring the FORMAT/genotype columns).

Best,
Sigve

[zacshi]

Thanks you for the prompt reply! Could you please let me know what instruction should be put in the toml file or somehow to disable VCF-validator? I tried vcf-validator = false, not working...

[sigven]

Hi,
By mistake I forgot to attach the default TOML config file in the pre-release, but it is present in the repo now: pcgr.toml. I suggest you download it and use it when running your sample.

If you read the documentation concerning the config file, you can see how different parts of the workflow can be configured (query tumor type, target region size, turning on/off different parts etc):
PCGR configuration file. These are important elements to consider, in order to get your report as meaningful as possible.

I merely set vcf_validation = false and successfully produced a report for you (can be downloaded here)

[zacshi]

Wonderful, thank you very much. I appreciate it!

[andreyurch]

Dear Sigven,

Thank you very much for this wonderful tool PCGR, I like it very much! The only one thing: do not you think that it would be better to keep this issue open, because Mutect2 is a standard tool in numerous laboratories? I tried the PCGR with turned off VCF validation, and it works, but doesnot show AF, DP and other important parameters for mutations... Would no be it possible to implement something Mutect2 - tolerating? :)