Question: vcf-annotate not adding annotations
0
gravatar for wes3985
2.1 years ago by
wes39850
wes39850 wrote:

I would like to annotate a vcf file with the output of a filter that detects false positives. I know a very similar question to this has been previously posted here but the answer did not work for my case. The vcf file was produced by varscan-2. Here is the first few rows of my vcf:

    ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand reads1plus)">
##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample1
chr1    13273   .       G       C       .       PASS    ADP=69;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:150:71:69:30:39:56.52%:8.7033E-16:37:37:22:8:37:2
chr1    13417   .       C       CGAGA   .       PASS    ADP=61;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:97:62:61:35:27:43.55%:1.9451E-10:34:34:0:35:0:27
chr1    14653   .       C       T       .       PASS    ADP=37;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:29:37:37:28:9:24.32%:1.1256E-3:34:35:27:1:9:0
chr1    15903   .       G       GC      .       PASS    ADP=35;WT=0;HET=0;HOM=1;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    1/1:118:35:35:8:27:77.14%:1.2926E-12:34:35:6:2:15:12
chr1    16495   .       G       C       .       PASS    ADP=17;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:38:18:17:7:10:58.82%:1.4831E-4:36:35:7:0:10:0

here is the first few lines of my annotation file:

CHROM  FROM    INFO/FP
chr1     13273   PASS
chr1     13417   NoReadCounts
chr1     14653   Strandedness
chr1     15903   NoReadCounts
chr1     16495   PASS
chr1     69511   PASS
chr1     129285          VarDist3
chr1     137622          PASS
chr1     137825          PASS

Common problems like the 'chr' being different in the files can be ruled out. in the tabix line I have specified 's' as 1 to specify where the chromosome name is, 'b' and 'e' as '2' because the documentation suggests to do this is only one position is supplied in the annotation file. Here is my code to attempt to get the annotation to work:

$bgzip annotation_file
$tabix -s 1 -b 2 -e 2 -f annotation_file.gz
cat vcf_file.vcf | vcf-annotate -a annotation_file.gz \
-d key=INFO,ID=FP,Number=1,Type=String,Description='fpfilter annotation' \
-c CHROM,FROM,INFO/FP > annot_vcf.vcf

And here is the output of the annotation process:

##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
##INFO=<ID=FP,Number=1,Type=String,Description="fpfilter annotation">
##source_20170210.1=vcf-annotate(v0.1.14-12-gcdb80b8) -a path/to/annotation_file.gz -d key=INFO,ID=FP,Number=1,Type=String,Description=fpfilter annotation -c CHROM,FROM,INFO/FP
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample1
chr1    13273   .       G       C       .       PASS    ADP=69;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:150:71:69:30:39:56.52%:8.7033E-16:37:37:22:8:37:2
chr1    13417   .       C       CGAGA   .       PASS    ADP=61;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:97:62:61:35:27:43.55%:1.9451E-10:34:34:0:35:0:27
chr1    14653   .       C       T       .       PASS    ADP=37;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:29:37:37:28:9:24.32%:1.1256E-3:34:35:27:1:9:0
chr1    15903   .       G       GC      .       PASS    ADP=35;WT=0;HET=0;HOM=1;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    1/1:118:35:35:8:27:77.14%:1.2926E-12:34:35:6:2:15:12
chr1    16495   .       G       C       .       PASS    ADP=17;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:38:18:17:7:10:58.82%:1.4831E-4:36:35:7:0:10:0

A line has been added above where the variants start giving details of what 'should' be in the annotation but there is no annotation added to the INFO column (or any other column). Any help or suggestions or would be much apreciated as this tool does not seem to work at all.

snp next-gen • 928 views
ADD COMMENTlink written 2.1 years ago by wes39850

Could you provide the first few lines of desired output? I think I have a workaround.

ADD REPLYlink written 2.1 years ago by Vincent Laufer1.0k
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