Release 0.3.4 missing column headers in annotated VCF #150
Description
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