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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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ERROR IN VCF HEADER #141

Open AqsaMajeed-star opened 4 years ago

AqsaMajeed-star commented 4 years ago

Verify

Subject of the issue

I ran bcftools merge tool for five of vcfs for which variants were called using samtools. The merged_vcf was used as input for FixVcfMissingGenotypes. Unfortunately, the scripts fails after a few seconds and outputs the following error: "htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file"

Your environment

Error Message

[SEVERE][Launcher]Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:115) at htsjdk.variant.vcf.VCFIteratorBuilder$VCFReaderIterator.(VCFIteratorBuilder.java:177) at htsjdk.variant.vcf.VCFIteratorBuilder.open(VCFIteratorBuilder.java:97) at com.github.lindenb.jvarkit.util.vcf.VCFUtils.createVCFIteratorFromInputStream(VCFUtils.java:288) at com.github.lindenb.jvarkit.util.vcf.VCFUtils.createVCFIterator(VCFUtils.java:326) at com.github.lindenb.jvarkit.util.jcommander.Launcher.openVCFIterator(Launcher.java:515) at com.github.lindenb.jvarkit.util.jcommander.Launcher.doVcfToVcf(Launcher.java:565) at com.github.lindenb.jvarkit.util.jcommander.Launcher.doVcfToVcf(Launcher.java:614) at com.github.lindenb.jvarkit.tools.misc.FixVcfMissingGenotypes.doWork(FixVcfMissingGenotypes.java:346) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:777) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:940) at com.github.lindenb.jvarkit.tools.misc.FixVcfMissingGenotypes.main(FixVcfMissingGenotypes.java:358) [INFO][Launcher]fixvcfmissinggenotypes Exited with failure (-1)

lindenb commented 4 years ago

what is the output of file your.vcf and

grep "#CHROM" your.vcf