VCF format 4.1 uncompressed file import fails with AC field error

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1

The following error is presented when trying to read uncompressed .vcf file, which is (VCFv4.1). Any ideas or workarounds if I want to convert this into a .vds?

is.hail.utils.HailException: encountered problem with file file:/scratch/files/blah/blah/blah/blah/blah/blah/chr2.pass.gtonly.minDP0.genotypes.vcf
  Your input file has a malformed header: Count < 0 for fixed size VCF header field AC
    at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:6)
    at is.hail.utils.package$.fatal(package.scala:27)
    at is.hail.io.vcf.LoadVCF$.apply(LoadVCF.scala:218)
    at is.hail.HailContext.importVCFs(HailContext.scala:557)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:280)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:214)
    at java.lang.Thread.run(Thread.java:748)

Hail version: 0.1-5c275cc
Error summary: HailException: encountered problem with file file:/scratch/files/blah/blah/blah/blah/blah/blah/chr2.pass.gtonly.minDP0.genotypes.vcf
  Your input file has a malformed header: Count < 0 for fixed size VCF header field AC
2

What is the INFO line for AC?

3 
##fileformat=VCFv4.1
##source=pseq
##INFO=<ID=AC,Number=-1,Type=Integer,Description="Allele count for each alternate allele">
##INFO=<ID=AF,Number=-1,Type=Float,Description="Frequency for each alternate allele (estimated from primary data, not called genotypes)">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Combined depth across samples">
##INFO=<ID=AVGDP,Number=1,Type=Float,Description="Average Depth per Sample">
##INFO=<ID=GC,Number=-1,Type=Integer,Description="Genotype Counts">
##INFO=<ID=GN,Number=1,Type=Integer,Description="Total Number of Genotypes">
##INFO=<ID=HWEAF,Number=-1,Type=Float,Description="Genotype likelihood based Allele Frequency assuming HWE">
##INFO=<ID=HWDGF,Number=-1,Type=Float,Description="Genotype likelihood based Genotype Frequency ignoring HWE">
##INFO=<ID=IBC,Number=1,Type=Float,Description="Inbreeding Coefficients calculated from genotype likelihoods">
##INFO=<ID=HWE_SLP,Number=1,Type=Float,Description="Signed log p-values testing  statistics based Hardy Weinberg ln(Likelihood Ratio)">
##INFO=<ID=ABE,Number=1,Type=Float,Description="Expected allele Balance towards Reference Allele on Heterozygous Sites">
##INFO=<ID=ABZ,Number=1,Type=Float,Description="Average Z-scores of Allele Balance towards Reference Allele on Heterozygous Sites">
##INFO=<ID=NS_NREF,Number=1,Type=Integer,Description="Number of samples with non-reference reads">
##INFO=<ID=BQZ,Number=1,Type=Float,Description="Correlation between base quality and alleles">
##INFO=<ID=CYZ,Number=1,Type=Float,Description="Correlation between cycle and alleles">
##INFO=<ID=STZ,Number=1,Type=Float,Description="Correlation between strand and alleles">
##INFO=<ID=NMZ,Number=1,Type=Float,Description="Correlation between mismatch counts per read and alleles">
##INFO=<ID=IOR,Number=1,Type=Float,Description="Inflated rate of observing of other alleles in log10 scale">
##INFO=<ID=NM0,Number=1,Type=Float,Description="Average number of mismatches in the reads with ref alleles">
...
4

I’m inclined to agree with wherever this error is coming from (probably htsjdk) that your VCF is malformed! If AC/AF fields don’t exist, try removing them from the header entirely

5

I will report back, thanks for the quick response

6

Removing the field just errors on the next field that is -1… and the next… and the next. Changing the value to A or G, based on VCF documentation solves the issue. Also, using . for any value also works. Sorry about the confusion. Works as advertised once the format notation has been corrected.