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+split-vep --include not able to properly filter float columns extracted from CSQ #2039

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SpikyClip opened this issue Nov 16, 2023 · 1 comment
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+split-vep --include not able to properly filter float columns extracted from CSQ #2039

SpikyClip opened this issue Nov 16, 2023 · 1 comment

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@SpikyClip
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Version: bcftools 1.18

Problem

When the following code is used, BCFtools +split-vep is unable to recognise the type of the field MAX_AF as Float and is therefore unable to filter MAX_AF.

bcftools +split-vep test.vcf -c 'MAX_AF:Float' -i 'MAX_AF<0.001'

[E::bcf_get_info_values] Unexpected type 7 at chr1:20815486
[E::bcf_get_info_values] Unexpected type 7 at chr1:20815541
[E::bcf_get_info_values] Unexpected type 7 at chr1:20815567
[E::bcf_get_info_values] Unexpected type 7 at chr1:20815861
[E::bcf_get_info_values] Unexpected type 7 at chr1:20816198
[E::bcf_get_info_values] Unexpected type 7 at chr1:20816713
[E::bcf_get_info_values] Unexpected type 7 at chr1:20817681
[E::bcf_get_info_values] Unexpected type 7 at chr1:20819475
[E::bcf_get_info_values] Unexpected type 7 at chr1:20821669
...

Expected Behavior

  • Produces an output filtered by the MAX_AF value

What I've tried

bcftools +split-vep test.vcf -d -c 'MAX_AF:Float' -i 'MAX_AF<0.001'
bcftools +split-vep test.vcf -c 'MAX_AF:FLOAT' -i 'MAX_AF<0.001'
bcftools +split-vep test.vcf -i 'MAX_AF<0.001'

I can confirm the column type is correct if I pass it through split-vep -c "-":

##INFO=<ID=MAX_AF,Number=.,Type=Float,Description="The MAX_AF field from INFO/CSQ">

What did work, however, was to +split-vep then pipe it to bcftools filter:

bcftools +split-vep test.vcf -c '-' | bcftools filter -i 'MAX_AF < 0.001'

At least there is a workaround but its still a bug that ought to get fixed. Apologies for not being able to provide a test file, but this should be reproducible on any vep annotated file I think.
@pd3 pd3 closed this as completed in 4014f7e Dec 1, 2023
@pd3
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pd3 commented Dec 1, 2023

Thank you for the bug report, this is now fixed.

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@pd3 @SpikyClip