Error: haps_proc_init region.c:20: failed to parse info header

[weishwu]

I was following the Ultima documentation to do germline variant calling. My understanding is that their tool wraps deepvariant, so I wonder if I could get help here.

• Command:

tool   \
    --input 15276_CV_16.final.cram \
    --cram-index 15276_CV_15.final.cram.crai  \
    --bed interval_0031.bed \
    --output 15276_CV_15.0031 \
    --reference Homo_sapiens_assembly38_noChr11random_primaryContigs.fasta \
    --min-base-quality 5 \
    --min-mapq 5 \
    --cgp-min-count-snps 2 \
    --cgp-min-count-hmer-indels 2 \
    --cgp-min-count-non-hmer-indels 2 \
    --cgp-min-fraction-snps 0.12 \
    --cgp-min-fraction-hmer-indels 0.12 \
    --cgp-min-fraction-non-hmer-indels 0.06 \
    --cgp-min-mapping-quality 5 \
    --max-reads-per-region 1500 \
    --assembly-min-base-quality 0 \
    --optimal-coverages 50 \
    --median-coverage 29 \
    --add-ins-size-channel

• Error: ERROR haps_proc_init region.c:20: failed to parse info header: " "start": 96724708,

The full log is attached.

make_examples.15276_CV_15.0031.log

Thanks.

[doron-st]

Hi @weishwu,

Ultima's code is based on deepvariant but is an independent re-write.
I understand you have contacted our tech support through a different communication channel.

Good luck!