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nygenome / lancet

Microassembly based somatic variant caller for NGS data
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Error: not able to jump successfully to the region's left boundary in tumor #38

Closed toedling closed 5 years ago

toedling commented 5 years ago

Hello, I am trying to run lancet (v1.0.7) on a pair of tumor/normal BAM files which were generated by aligning whole-genome seq data using "bwa mem". The BAM files are OK, all other tools that I checked work fine with them. Chromosomes are named "chr1...chrX".

When running the following command lancet --tumor $TUMORBAM --normal $CONTROLBAM --ref $GENOMEFA \ --reg chr1 --num-threads 1 >chr1.vcf

I get this error message

starting thread 1 on 2489560 windows Process reads Error: not able to jump successfully to the region's left boundary in tumor

Do you have any idea how that error might arise and how I could avoid it? Thanks in advance.

gnarzisi commented 5 years ago

Are the chromosome labels in the reference genome FASTA file matching with the BAM?

toedling commented 5 years ago

Yes, the chromosome labels are the same. In this case I had used --reg chr1, and "chr1" is the label used for the first chromosome both in the BAM files and in the genome Fasta file.

gnarzisi commented 5 years ago

Thanks for checking.

Can you reproduce the error using small BAMs extracted from the tumor and the normal? If you can share them with me, together with the reference used to aligned the data, I will be able to debug the problem on my side.

gnarzisi commented 5 years ago

Closing the ticket, but feel free to reopen if you still haven't solved your issue.