incompatible with the VCF file error

DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)

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incompatible with the VCF file error #237

Open a00101 opened 4 years ago

a00101 commented 4 years ago

Dear, hisat2 team

Error: the reference genome you provided seems to be incompatible with the VCF file at 154559100 of chromosome chrX where g is in the reference genome while G is in the VCF file

I got above errors from customed VCFfile from GATK ver3. I used the same reference genome GRCh38. Can I ignore this issue or modifiy something. If I should fix this error, please help me out.

Thanks.

ZHIDIHUAYUAN commented 3 years ago

I have the same problem. Have you figured it out?

yjiang296 commented 1 year ago

Hello, I wonder have you fix it? Or I can just ignore this error?