Subset specific TAGS

[mh11]

These changes allow to customise the naming of tags and calculation of alleles by providing

• a custom prefixes for tags
• a list of sample IDs to calculate the tags for

Combined usage (prefix + samples)

By using these options in combination allows the calculation of e.g. EUR, SAS and * EAS* samples on the fly.

bcftools +fill-tags my.vcf.gz -- \
-S EUR_,my_eur.txt -S NOT_EUR_,^my_eur.txt \
-S SAS_,my_sas.txt \
-S EAS_,my_eas.txt | \
bgzip > my_annotated.vcf.gz

Prefix

Using a prefix ABC_ all tags (incl. description) will have the prefix added.
e.g. ABC_AN=.., ABC_AC=..,

Samples

Using a sample list allows the calculation of TAGS specific to this group of samples.
e.g. -S my_list.txt

[pd3]

Hi, thank you for this pull request. There is a related plugin which should be merged with fill-tags at some point. Could you perhaps modify your pull request according to that? It is more general in that it annotates multiple populations simultaneously.

[mh11]

Thanks for the suggestion - your related plugin is very similar in this sense. I’ll give it a go to modify the pull request.

On 24 Oct 2016, at 18:19, pd3 notifications@github.com wrote:

Hi, thank you for this pull request. There is a related plugin which should be merged with fill-tags at some point. Could you perhaps modify your pull request according to that? It is more general in that it annotates multiple populations simultaneously.

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[mh11]

The latest commit gives you the flexibility to use multiple ID list in different ways (include/exclude) to annotate vcf files with custom headers.

[pd3]

Thank you for this. Can you please check the failing tests?

[mh11]

Done - checks are updated, additional test added and all passing.

[pd3]

Hi, just added a minor improvement in -S initialization (1322e04) and merged. This pull request can be now closed. Thanks for this!