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This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
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bcftools consensus throws "Failed to parse TBX_GENERIC" #789

Closed andreas-wilm closed 6 years ago

andreas-wilm commented 6 years ago

Dear all,

I get the following error with attached files and bcftools 1.6 and 1.8, but not with 1.3:

bcftools consensus -f cons.X8vZEo.0.fa test.vcf.gz
[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used?
The offending line was: "PDH205_CGTACG-gap-filled-assembly      7       .       G       T       49314   PASS    DP=1814;AF=1;SB=0;DP4=0,0,1380,434"

Worst of all, bcftools terminates but with exit code 0.

All other bcftools commands and tabix itself work

Andreas

andreas-wilm commented 6 years ago

Looks like tabix didn't like this vcf file. It got processed without warning, but apparently not as vcf. So bcftools consensus (and probably other subcommands depending on the index) choked. Indexing with force type helped. Closing

andreas-wilm commented 5 years ago

Hello, as mentioned there the trick is to recreate the index. Andreas

On Tue, 30 Apr 2019, 18:29 jgarces, notifications@github.com wrote:

Hi @andreas-wilm https://github.com/andreas-wilm, I've got the same problem and I cannot solve it... neither forcing type or whatever other think. Any idea, please? Thanks!

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