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brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5
MIT License
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Release 0.3.4 missing column headers in annotated VCF #150

Closed bangbangphil closed 1 year ago

bangbangphil commented 1 year ago

With release 0.3.4, written VCF is missing column headers. I have attached a simple example to show this. Here is the output VCF with release 0.3.4 (truncated): 

##fileformat=VCFv4.2
##INFO=<ID=COSMIC_CNT,Number=.,Type=String,Description="calculated by uniq of overlapping values in field CNT from cosmicdb.vcf.bgz">
##vcfanno=0.3.4
FORMAT  22-00607-DNA_S4.bam
chr1    162754716   .   C   T   100.0   PASS    CSQR=1|ENSR00000014894|regulatory_region_variant;CSQT=1|DDR2|NM_006182.2|missense_variant;DP=182;phyloP=0.317   GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:154,28:182:0.154:20:-100.0000:0.0055
chr2    15944889    .   C   CTCTGTCTCTTA    100.0   SB  CSQT=1|MYCNOS|NM_001329968.1|upstream_gene_variant,1|MYCN|NM_005378.5|intron_variant;DP=174 GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:133,41:174:0.236:20:-2.3132:0.0000

Note the missing/malformed column label header line.

And here is the VCF output from same run case using release 0.3.3:

##fileformat=VCFv4.2
##INFO=<ID=COSMIC_CNT,Number=.,Type=String,Description="calculated by uniq of overlapping values in field CNT from cosmicdb.vcf.bgz">
##vcfanno=0.3.3
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  22-00607-DNA_S4.bam
chr1    162754716   .   C   T   100.0   PASS    CSQR=1|ENSR00000014894|regulatory_region_variant;CSQT=1|DDR2|NM_006182.2|missense_variant;DP=182;phyloP=0.317   GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:154,28:182:0.154:20:-100.0000:0.0055
chr2    15944889    .   C   CTCTGTCTCTTA    100.0   SB  CSQT=1|MYCNOS|NM_001329968.1|upstream_gene_variant,1|MYCN|NM_005378.5|intron_variant;DP=174 GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:133,41:174:0.236:20:-2.3132:0.0000

thanks!

Phil

bangbangphil commented 1 year ago

Missing attachment sample.tar.gz

brentp commented 1 year ago

Wow. Not sure how this got through. Thanks very much for taking the time to report. I added tests for this both here and in brentp/vcfgo, which is where the source is. I think I had a stale vcfgo last release. Would you verify that the attached binary works for you and I'll make a new release. vcfanno_linux64.gz (just gunzip, and chmod +x)

bangbangphil commented 1 year ago

You're welcome, and thank you for the quick reply and fix. I just tested it and the generated VCF is as expected, with appropriate column headers. Should be good to go! Thanks for this nice tool, it's such a swift method to incorporate any database in an annotation pipeline. Really useful!

brentp commented 1 year ago

I pushed the release. Thanks again!