How does one create a custom VCF file?

Question

[manfi]

I'm running an analysis where I use Mutect2 to look for reads that code for a particular pathogenic variant. The variant is given in a VCF file (here: myvcf.vcf.gz).

gatk Mutect2 \
  -R "hg38.fa" \
  --alleles "myvcf.vcf.gz" \
  -L "myvcf.vcf.gz" \
  -I "input.bam" \
  -O "output.vcf"

For "myvcf.vcf.gz" I initially used a VCF file which I generated with a different analysis, this worked well (tags omitted for brevity):

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  312092_13-Ctrl30_G01_S16_R1_001.fastq.gz
chr20   4699818 .   G   A   222.391 .   DP=1064;VDB=0.670108;SGB=-0.693147;RPBZ=-0.800274;MQBZ=-1.6155;MQSBZ=-4.79102;BQBZ=9.03611;SCBZ=0.192787;FS=0;MQ0F=0;AC=1;AN=2;DP4=214,222,177,203;MQ=59    GT:PL:AD    0/1:255,0,190:436,380

Now I want to look for a new variant. I haven't got a VCF file, so I simply copied the information on this variant from Ensembl and generated the following:

##fileformat=VCFv4.3
##fileDate=20240306
##source=Ensembl
##reference=GRCh38
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT
20      4699752 rs74315403  G   A   .    .      .      GT

However, Mutect2 gave me the error below. It seems like my custom VCF lacks genotype/sample data.

So my question is: How do I create a correctly formatted VCF file for the purpose of this analysis?

org.broadinstitute.hellbender.exceptions.GATKException: Error initializing feature reader for path /add/results/2024-03-05_ref_VCFs_for_mutations/D178N.vcf.gz
        at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:436)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:377)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:319)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:291)
        at org.broadinstitute.hellbender.engine.FeatureManager.addToFeatureSources(FeatureManager.java:245)
        at org.broadinstitute.hellbender.engine.FeatureManager.initializeFeatureSources(FeatureManager.java:208)
        at org.broadinstitute.hellbender.engine.FeatureManager.<init>(FeatureManager.java:155)
        at org.broadinstitute.hellbender.engine.GATKTool.initializeFeatures(GATKTool.java:497)
        at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:726)
        at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:79)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:147)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
        at org.broadinstitute.hellbender.Main.main(Main.java:306)
Caused by: htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: The FORMAT field was provided but there is no genotype/sample data, for input source: /add/results/2024-03-05_ref_VCFs_for_mutations/D178N.vcf.gz
        at htsjdk.tribble.TabixFeatureReader.readHeader(TabixFeatureReader.java:97)
        at htsjdk.tribble.TabixFeatureReader.<init>(TabixFeatureReader.java:82)
        at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:117)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:433)
        ... 15 more

Answer 1

[Pierre Lindenbaum]

The FORMAT field was provided but there is no genotype/sample data,

remove the whole column FORMAT, including the header.

gunzip -c "myvcf.vcf.gz" | cut -f 1-8 | bcftools view -O z -o new.vcf.gz && bcftools index -t  new.vcf.gz