This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
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
...
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.
Version: bcftools 1.18
Problem
When the following code is used,
BCFtools +split-vep
is unable to recognise the type of the fieldMAX_AF
asFloat
and is therefore unable to filterMAX_AF
.Expected Behavior
What I've tried
I can confirm the column type is correct if I pass it through
split-vep -c "-"
:What did work, however, was to
+split-vep
then pipe it tobcftools filter
: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.