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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Error: Haplotype is too short for alignment #133

Closed DiDeoxy closed 3 years ago

DiDeoxy commented 3 years ago

Describe the bug Error: Haplotype is too short for alignment

Version

$ octopus --version
octopus version 0.7.0 (develop 302c444d)
Target: x86_64 Linux 3.10.0-1127.8.2.el7.x86_64
SIMD extension: AVX2
Compiler: GNU 10.2.0
Boost: 1_73

Command Command line to install octopus:

$ ./octopus/scripts/install.py --prefix ~/bin -D

Command line to run octopus:

$ octopus \
        -R $reference \
        -I $bam \
        -T chr1H chr2H chr3H chr4H chr5H chr6H chr7H \
        --refcall \
        --debug \
        --sequence-error-model PCR.HiSeq-2500 \
        -o ${sample_id}.g.vcf

Additional context Add any other context about the problem here, e.g.

octopus_debug.zip

dancooke commented 3 years ago

Thanks for the bug report. Are you able to share the BAM file? The error occurs around chr3H:449833583 so just a section around there (say chr3H:449823583-449843583) should be enough to reproduce.

DiDeoxy commented 3 years ago

error_region_ERR2221531.zip

A 2Mb region centered on the spot, let me know is you need more.

dancooke commented 3 years ago

Thanks. Should be fixed in d300da7659e50700cf4a68ddbc4c6d1cd836aa62. Please re-open if any further problems.