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missing t_depth/t_alt_count/t_ref_count fields in MAF files #240

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ltang217 opened this issue Jan 10, 2020 · 2 comments
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missing t_depth/t_alt_count/t_ref_count fields in MAF files #240

ltang217 opened this issue Jan 10, 2020 · 2 comments
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@ltang217
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hi, I have problem getting t_depth/t_alt_count/t_ref_count information for all SNVs from VCF files. I checked that my vcf file does contain 'GT:AD:AF:DP' under tumor sample column, but in the converted maf file, some variants get 't_depth/t_ref_count/t_alt_count', but some others not. And this happens on both SNV and small INDELs. Very confusing. Anyone can help look into this? I can provide the sample vcf files. Thanks!

@ckandoth ckandoth self-assigned this Apr 20, 2020
@ckandoth
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ckandoth commented Apr 20, 2020

@ltang217 this usually happens if you forget to specify --tumor-id or --vcf-tumor-id. If that is not the issue, then please share your command-line usage, and a sample VCF. Thanks.

@sunqiangzai
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@ckandoth, Thank you for your advice, add --vcf-tumor-id and --vcf-normal-id works.

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