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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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bam file error when running "msisensor-pro baseline" step #46

Open YXbioinfor opened 2 years ago

YXbioinfor commented 2 years ago

Dear author ： i got a very strange error when i runing
msisensor-pro baseline -d $ref_list/reference.list -i configure.txt -o ./ Open bam file failed( ), please provide valid bam file with its index file ! it seem to say that i have to set index file for every bam file, so i use samtools index to do this then i got .bai index files for every bam file. then I repat the code agagin ,however the same error happend where i was wrong?! thank you for your answer

PengJia6 commented 1 year ago

Did you give correct path of the bam file?

nservant commented 9 months ago

Hi, I think I have the same issue, which is due to the fact that the code is using real path ... For instance, if you put in the same folder two bam/bai using symbolic links, pointing to the files in different folders, MSIsensor is not able to match them. This is because it goes through the real path of the files.