Uploading germline VCF data into cBioPortal

[Abhijeet Malatpure]

Hello cBioPortal gurus,

I have a cache of VCF files for germline samples that I would like to upload into a study on my local cBioPortal instance. They all have the following format:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  858444493-fy5hF6Dg

chr1    51972   .       GGAC    G       18      PASS    .       GT:AD:DP        1/1:0,6:6

chr1    121269  .       CT      C       70      PASS    OLD_VARIANT=1:121269:CTT/CT     GT:AD:DP        0/1:7,6:13

chr1    275583  .       TTTTA   T       99      PASS    OLD_VARIANT=1:275583:TTTTATTTATTTA/TTTTATTTA    GT:AD:DP        0/1:7,18:25

chr1    609440  .       C       T       99      PASS    .       GT:AD:DP        0/1:25,7:32

chr1    630555  .       C       T       99      PASS    .       GT:AD:DP        0/1:21,21:42

chr1    638771  .       A       T       99      PASS    .       GT:AD:DP        0/1:21,15:36

chr1    739602  .       A       AT      65      PASS    .       GT:AD:DP        0/1:15,5:20

chr1    749482  .       G       A       99      PASS    .       GT:AD:DP        0/1:17,7:24

chr1    757414  .       CA      C       13      PASS    .       GT:AD:DP        0/1:4,2:6

chr1    779968  .       T       G       99      PASS    .       GT:AD:DP        1/1:0,33:33

chr1    782207  .       G       A       99      PASS    .       GT:AD:DP        0/1:8,13:21

chr1    788418  .       CAG     C       87      PASS    .       GT:AD:DP        1/1:0,29:29

....

where 858444493-fy5hF6Dg is the germline sample ID.

I used VCF2MAF to convert these VCF files to MAF with the sample ID as --vcf-normal-id, and then merged them together in the end. However, the metaImport process shows the following error:

ERROR: data_mutations.maf: lines [3, 5, 11, (11209 more)]: column 16: Value in column 'Tumor_Sample_Barcode' is invalid; value encountered: ''

How should I correctly process germline data to be uploadable into cBioPortal?

Regards,

Abhi

[JJ Gao]

Hi Abi,

Would you please include a few lines of your MAF file for us to take a look at?

Thanks,

-JJ

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[Abhijeet Malatpure]

Hi JJ,

Please find a Germline MAF file attached here.Thank you for looking into this.

Best,

Abhi Malatpure

[JJ Gao]

Hi Abhi,

It looks like the column "Tumor_Sample_Barcode" is empty. This can be addressed by following the steps on sample IDs https://github.com/mskcc/vcf2maf. Please let us know if you have additional questions.

Best,

-JJ

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[Malatpure, Abhijeet]

I used VCF2MAF to convert the germline VCF files to MAF. However, because they are germline samples (not tumor), I mapped them to the Matched_Norm_Sample_Barcode field during conversion instead. 

Is this not the correct way to process it?

Regards,

Abhi

On Feb 8, 2021, at 6:40 PM, JJ Gao <jianji...@gmail.com> wrote:



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[JJ Gao]

I see. We are actually not importing the Matched_Norm_Sample_Barcode and Tumor_Sample_Barcode is required. A workaround would be add the normal sample id as tumor id.