Closed MikeHala closed 2 years ago
I can't recreate this below is what I do. I suspect your file is index incorrectly. Note how I index below:
wget -qO - https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh38/whole_genome_SNVs.tsv.gz | zcat - | head -2000 | bgzip -c > whole_genome_SNVs.tsv.gz
tabix -f -b 2 -e 2 -s 1 whole_genome_SNVs.tsv.gz
echo -e "##fileformat=VCFv4.2
#CHROM POS ID REF ALT QUAL FILTER INFO
1 10110 id A G 46 PASS ." > x.vcf
echo '
[[annotation]]
file="whole_genome_SNVs.tsv.gz"
names=["CADD_phred"]
ops=["mean"]
columns=[6] ' > bug.conf
vcfanno bug.conf x.vcf | grep -v ^#
if you edit this in such a way that you can demonstrate the bug, then we can track it down.
BTW, there is no need to add/remove "chr" as vcfanno
will match "chr1" with "1", for example.
here it is in a file so you don't need to worry about the tabs bug.sh.gz
Thanks for the quick reply, Brent!
It seems to work now (note for future readers - the toy VCF above should be tab, not space separated)
=============================================
vcfanno version 0.3.3 [built with go1.16.5]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:116: found 1 sources from 1 files
vcfanno.go:157: falling back to non-bgzip
vcfanno.go:250: annotated 1 variants in 0.00 seconds (366.7 / second)
1 10110 id A G 46.0 PASS AC=1;AF=0.5;AN=2;CADD_phred=8.752
Will re-index the CADD file as you do and will let you know how it goes!
Thanks again, Mike
Happy to confirm that after re-compressing the CADD v1.6 scores file with bgzip and tabix indexing it following your recipe it works as expected!
Thanks again for your help! Mike
great! thanks for following up.
Hi,
I am trying to annotate my VCF file (biallelic SNPs only, edited to remove the chr prefix of the chromosome name for each variant to match the CADD naming convention) with CADD v1.6 and running to problems as in issue #137 , i.e. CADD_phred is included in the header but no annotations were added to the variant INFO field.
I have re-indexed the CADD file with tabix (as suggested in #137), but still no luck.
My CADD.conf file:
I have also tried replacing
columns=[6]
withfields=["PHRED"]
.Here the first lines of the CADD file : whole_genome_SNVs.tsv.gz
Here is an example variants from the query file
1 34165788 chr1_34165788_C_G C G 46 PASS CSQ=G|missense_variant&NMD_transcript_variant|MODERATE|CSMD2|ENSG00000121904|Transcript|ENST00000241312|nonsense_mediated_decay|1/70||||55|26|9|G/A|gGc/gCc|||-1||HGNC|HGNC:19290|||||,G|upstream_gene_variant|MODIFIER|C1orf94|ENSG00000142698|Transcript|ENST00000373374|protein_coding|||||||||||1095|1||HGNC|HGNC:28250|||||,G|upstream_gene_variant|MODIFIER|CSMD2|ENSG00000121904|Transcript|ENST00000373381|protein_coding|||||||||||514|-1||HGNC|HGNC:19290|YES||||,G|missense_variant|MODERATE|CSMD2|ENSG00000121904|Transcript|ENST00000373388|protein_coding|1/70||||55|26|9|G/A|gGc/gCc|||-1||HGNC|HGNC:19290|||||,G|missense_variant|MODERATE|CSMD2|ENSG00000121904|Transcript|ENST00000619121|protein_coding|1/71||||55|26|9|G/A|gGc/gCc|||-1||HGNC|HGNC:19290|||||;AF=0.00119988;AN=20002;AC=24;<20x AN_subpop values>;<20x AF_subpop values>;<20x AC_subpop values> GT 0/0 .....
Command I used:
time vcfanno_linux64 -p 2 CADD.conf query.vcf > query.CADD.vcf
Output of the tool:
Output of
tabix /full/path/to/whole_genome_SNVs.tsv.gz 1:34165788-34165789
isAny suggestions what I am doing wrong would be greatly appreciated!
Best, Mike