For mislabelled Tumor & Normal bam files from same patient, which gatk tool approach can i use to reclassify?
Please if I have mislabelled bam files (1 should be tumor & the other germline bam file) from same patient which approach or gatk tool can i use to correctly reclassify tumor & germline bam files?
Thank you in advance for your help
-S
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Hi sahuno,
Are you looking to just rename your files? You can do this by editing the text of the header and then replacing the header of your files using the Picard tool ReplaceSamHeader. Are there other things you would need to change that I am not thinking of, or does this solve your issue?
Best,
Genevieve
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No please, the samples may have been mislabeled. can I tell from the reads or something if this is likely to be tumor or normal?
-S
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I'm not exactly sure, but you could check out the Picard tool CheckFingerprint, as it can be used to detect sample swaps.
The paper documenting this tool: https://www.nature.com/articles/s41467-020-17453-5
Here is a forum post with some explanation of how to use the outputs: https://gatk.broadinstitute.org/hc/en-us/community/posts/360058443032-Interpretting-CrosscheckFingerprints-metrics
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sahuno does that tool solve your issue?
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