Microsatellite Instability: msiSENSOR

Question

[sruthi]

Hi, I'm new to Microsatellite instability and trying to work on msiSENSOR tool. I tried uploading a bam file in msisensor using the command:

msisensor -d microsatellites.list -t tumor.bam -o output.tumor.prefix

And it says: failed to open homopolymers and microsatellites file I checked the path and it is correct. Could any one tell me what has gone wrong and how I must troubleshoot?

TIA

[sruthi]

Command:

msisensor -d microsatellites.list -t tumor.bam -e bed.file -o output.tumor.prefix

[sruthi]

The error is rectified.

[sruthi]

Hi, I was calculating MSI for tumor only sample using the below command:

msisensor msi -d microsatellites.list -t tumor.bam -e bed.file -o output.tumor.prefix

It shows:

[bam_index_load] Fail to load BAM index I checked the location of files and everything is in the same directory. Could anyone tell me where I have gone wrong and what must be done? TIA

[sruthi]

And it also says,

Assertion 'idx' failed Aborted core dumped.

[sruthi]

Hi all, I'm calculating MSI for tumor only sample using the below command: msisensor -d microsatellites.list -t tumor.bam -e bed.file -o output.tumor.prefix

I have tried the command for 3 different files and getting 0 for Number of MSI sites. Is there something that I've done wrongly? TIA

Answer 1

[sruthi]

When running msisensor msi command, the following error pops up. How should I take it further.

msisensor: bamreader.cpp:184: bool ReadInBamReads(const char*, conststring&, unsigned int, unsigned int, std::vector<split_read>&, std::string): Assertion `idx' failed. Aborted (core dumped)