Floating point exception when running version 1.0.4

[chisqr]

Hello,

I am running somatic sniper version 1.0.4 and am getting the following error:

Preparing to snipe some somatics
Using prior probabilities
Normal bam is normal.bam
Tumor bam is tumor.bam
Floating point exception

I have aligned the data using novoalign and have done base quality recalibration and indel realignment using GATK. I can visualize the BAM files in IGV too. I really hope if some one can help me with this.

regards,
Rahul

[ernfrid]

Sounds like a bug to me. I have not seen this in recent memory. My best guess is that this could be related to Novoalign as we've been running this with BWA extensively and haven't encountered this issue.

Any chance that you could provide a very small subset of the BAM file that replicates the error?
Can you tell me what operating system you're running on?

[chisqr]

Hello,

I was using the fasta file that came along wiht the GATK bundle. The .fai file there is not indexed using samtools 0.1.6 which is bundled with somatic sniper. I reindexed the fasta file using the 0.1.6 version of samtools and now somatic sniper is working!

regards,
Rahul