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wwylab / MuSE

Somatic point mutation caller
GNU General Public License v2.0
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`bgzip` issue during `MuSE sump` #5

Closed maotian06 closed 1 year ago

maotian06 commented 1 year ago

@jiyunmaths This error occurred during the MuSE sump process when processing both WGS and WXS samples. However, this is unstable and cannot be reproduced regularly during multiple test runs. The error message is:

  Was bgzip used to compress hg38_All_20180418.vcf.gz?
jiyunmaths commented 1 year ago

@maotian06 . Thanks for your comment. Sorry I have not met this issue. I'd like to suggest doing the following steps for the dbsnp 

gzip -d hg38_All_20180418.vcf.gz
bgzip -c hg38_All_20180418.vcf > hg38_All_20180418.vcf.gz
tabix -p hg38_All_20180418.vcf.gz
maotian06 commented 1 year ago

Thanks for the suggestion! @jiyunmaths This is not a stable error, and once I switched to the latest dbSNP, this didn't happen. I will let you know if this error occurs again.