output truncated

[ngfel...@gmail.com]

Hi,

I'm using vcfanno to annotate my *.vcf.gz file with ExAC information but ran into an issue and hope you can help. The program ran without error but the output I'm getting is truncated. For rows of data with ExAC annotation, here is an example output:

;exac_af=8.347e-05;exac_ac_het=4;exac_hom=0;exac_vqslod=-0.8627

The other fields are missing from the rows that have been annotated. The same number of lines are returned and rows without ExAC annotation are returned 'as is'.

Here are the first few lines of my vcf file:

##fileformat=VCFv4.2

###INFO=<ID=SMPL,Number=1,Type=String,Description="Sample ID">

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO

chr1    930253  .       C       A       39.6    .       SMPL=2-515765

chr1    931053  .       G       A       38.7    .       SMPL=2-515992

chr1    935767  .       T       G       38.6    .       SMPL=2-515579

chr1    939121  rs199625867;COSM912848  C       T       37.2    .       SMPL=F13_02862_004

Here is my conf.toml file:

[[annotation]]

file="ExAC_latest.vcf.gz"

fields = ["AF", "AC_Het", "AC_Hom", "VQSLOD"]

ops=["self", "self", "self", "self"]

names=["exac_af", "exac_ac_het", "exac_hom", "exac_vqslod"]

Command used:

./vcfanno_linux64 -p 8 conf.toml vardict.pass.vcf.gz > vardict.pass_annotated_2.vcf

Cheers,
Felicia

[Brent Pedersen]

Hi Felicia, I have tried to reproduce this but have not been able to.
Can your provide the smallest portion of ExAC_latest.vcf.gz that will
demonstrate the error?
And can you verify that you are using the latest vcfanno release?

Note that your pasted VCF has :
###INFO=<ID=SMPL,Number=1,Type=String,Description="Sample ID">
which has an extra '#' at the start, but this does not seem to affect
the result.

-Brent

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[ngfel...@gmail.com]

Hi Brent,

Thanks for your reply.

Please find attached a minimal vcf file. I ran vcfanno using this file and it had the same issue.

Cheers,
Felicia

[Brent Pedersen]

Hi, thanks for providing the file. This file is not sorted. Is the
real file sorted?
If you have out-of-order blocks with an old tabix index, that could be
the problem.
-B

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[ngfel...@gmail.com]

Hi Brent,

Sorry about that. I used 'shuf' to randomly select rows from the original file but I have now sorted the vcf. Please see attached.

Thanks,
Felicia