No header in VCF file
Hello everyone,
I am working with a specific variant calling pipeline, and the output is a VCF file missing headers.
It seems there are no option to add the header in the output.
Trying to add an header with picard FixVcfHeader, I get errors as shown below.
Would anyone have an idea what is missing with FixVcfHeader? Or knowing any tool that could add the header to the VCF file?
Exception in thread "main" htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw a header line specifying VCF version, for input source: file:///~/output.vcf
at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:263)
at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:102)
at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:127)
at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:121)
at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:81)
at htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:145)
at htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:95)
at picard.vcf.FixVcfHeader.doWork(FixVcfHeader.java:113)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:303)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
Caused by: htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw a header line specifying VCF version
at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:108)
at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:79)
at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:37)
at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:261)
... 10 more
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