I am having some problems with some of WGS cram files while accessing them with samtools. I checked a few of them and found that the crams are truncated, and I can't access chrM for example and samtools view returned a cram truncated error. I had problems with 49 of 200K crams, I believe all 49 had this problem.
Our support team is now in contact with you to verify the issue. If they could reproduce that, our Data team would get in touch with UKB to identify all problematic files and release the correct data.
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@Yong Qian?,
For reporting an issue with data, please forward this Community post to ukbiobank-support@dnanexus.com.
Our support team is now in contact with you to verify the issue. If they could reproduce that, our Data team would get in touch with UKB to identify all problematic files and release the correct data.
@Yong Qian? The corrupted data is now replaced with the valid data in our latest 13.1 data release. You can refresh the project to get them. See https://community.dnanexus.com/s/question/0D5t000004CaydsCAB/have-questions-about-the-gel-or-topmed-impute-data-release-ask-them-here
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