Hello, I was wondering if we can still access those unfiltered vcfs for UAMS in sub1? When I try to read vcf files for UAMS, this error shows up ``` Error: scanVcf: scanVcf: scanTabix: read line failed, corrupt or invalid file? path: test-data/_EGAR00001321728_EGAS00001001147_D2BEPACXX_6_687.MarkDuplicates.mdup..ANNOTATED.vcf.gz index: test-data/_EGAR00001321728_EGAS00001001147_D2BEPACXX_6_687.MarkDuplicates.mdup..ANNOTATED.vcf.gz.tbi path: test-data/_EGAR00001321728_EGAS00001001147_D2BEPACXX_6_687.MarkDuplicates.mdup..ANNOTATED.vcf.gz ``` Thanks in advance for your help! Jiayi

Created by Jiayi Bao jiayimiao0313
Dear organizer, It would be very nice if the UAMS tabix files can be fixed. Thank you very much for your time and patience! Regards, Jiayi
Thank you for your reply, Jincheng !!
I have the same issue when using `VariantAnnotation` to parse variant. I think this is due to the vcf index file is corrupted or somehow, and it only appears for UAMS dataset. I switched to `vcfR` for vcf file parsing to resolve this issue. `VariantAnnotation` does not seem to have option to suppress using tabix file if it is detected in the folder. It would be better if the organizers can check the UAMS tabix files, `VariantAnnotation` is a better package when we need to format variant annotation, 8X faster than `vcfR` function `INFO2df`. Good luck, Jincheng

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