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speed up bcftools annotate command

I'm annotating whole genome VCFs with dbSNP identifiers with the following command:

bcftools annotate -a "indexed VCF.gz" -c ID "target indexed VCF.gz" > "output.vcf"

this works perfectly, but takes about 15 minutes on our server (all data on ssd based partitions). For small target VCFs containing for example a target region on chrY it helps to add the region to the command with -R regions.txt, but not for larger genome wide VCFs.

Is there any way to speed up the annotation process?

next-gen snp bcftools
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updated by robby.concha-eloko • robby.concha-eloko • written by Fenny • Fenny

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

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written by Ram Ram

Hi, did you try GNU parallel? Here are some examples. I have good experiences to speed up all my processing tasks with parallel.

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written by Paul Paul

Where do you recommend using the BCF format? As the output format, or as the annotation file or as the input file? How does that compare against using a VCF in those places, and what about the VCF <-> BCF (or vice versa) conversion times? Please give us more details on your suggestions.

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written by Ram Ram

--threads INT Use multithreading with INT worker threads. The option is currently used only for the compression of the output stream, only when --output-type is b or z. Default: 0.

as OP generates uncompressed VCF, this option would be useless

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written by Pierre Lindenbaum Pierre Lindenbaum

Ok, thanks for the clarification. So just to make sure I understand. If I have say 2 bcfs:

a.bcf and b.bcf

I go:

bcftools merge --threads 64 a.bcf b.bcf -Ob > merged.bcf

Am I right in understanding that a.bcf and b.bcf are decompressed with one thread, then merged, and the 64 threads are used to convert the stream of that merged bcf into merged.bcf?

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written by curious curious

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