Combining Multiple Annotations using Streams (Piped input) fails

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
38/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
cli

Research direction

Start by reproducing the two-command bcftools annotate pipeline shown in the issue and trace how annotate opens piped input from stdin. Check whether the failure is expected for the supplied stream format or indicates unsupported pipe handling. Done means establishing supported behavior and resolving the error or documenting the limitation clearly.

Written by the indexing model from the issue text.

Description

enhancement P2: Desirable

Hi, I am trying to chain together multiple annotations using streams, for example:

bcftools annotate -Ou -a whole_genome_SNVs.add-chr.otoscopev6v7.tsv.gz -c CHROM,POS,ID,REF,ALT,CADD_RAW,CADD_PHRED -h CADD.vcf.header GJB2.CEPH.104_1-12_2-1330_1.unifiedGenotyper.vcf.gz | bcftools annotate -a ExAC.r0.3.sites.vep.vcf.gz

When doing this, I always receive an error:
Failed to open -: not compressed with bgzip

Is this type of operation not supported, or am I making a mistake in how I am running the annotations? Running each annotation independent of one another seems to work.

Thanks so much for your help!

Dominant language
C
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Forks
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Avg merge
2d 23h
Merged PRs (30d)
2

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