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biopet / vcffilter

MIT License
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Not clear how to use some flags #12

Open moldach opened 3 years ago

moldach commented 3 years ago

I've got a number of 0/0, 0/0, 0/0 reported in a VCF file so I will need to do some filtering.

I've never used vcffilter before and the manual isn't very clear for some parameters:

--deNovoInSample <sample>
                           Only show variants that contain unique alleles in complete set for given sample
  --deNovoTrio <child:father:mother>

It's not clear to me what I'm supposed to put in <sample> for example.

My VCF header looks like:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ./proband_bwaMEM_sort_dedupped.bam dad_bwaMEM_sort_dedupped.bam mom_bwaMEM_sort_dedupped.bam

$ java -jar ~/bin/vcffilter.jar -I proband_freebayes_filt_normalized_decompose.vcf -o filter.vcf --deNovoInSample proband

INFO  [2020-10-20 14:01:37,360] [VcfFilter$] - Start
Exception in thread "main" htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: /gpfs/home/moldach/projects/saliva/ensembl/deconseq/RUFUS-TRIO/proband_freebayes_filt_normalized_decompose.vcf, for input source: file:///gpfs/home/moldach/projects/saliva/ensembl/deconseq/RUFUS-TRIO/proband_freebayes_filt_normalized_decompose.vcf
    at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:262)
    at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:101)
    at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:126)
    at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:110)
    at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:74)
    at htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:117)
    at htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:68)
    at nl.biopet.tools.vcffilter.VcfFilter$.main(VcfFilter.scala:45)
    at nl.biopet.tools.vcffilter.VcfFilter.main(VcfFilter.scala)
Caused by: java.nio.file.NoSuchFileException: /gpfs/home/moldach/projects/saliva/ensembl/deconseq/RUFUS-TRIO/proband_freebayes_filt_normalized_decompose.vcf
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
    at java.nio.file.Files.newByteChannel(Files.java:361)
    at java.nio.file.Files.newByteChannel(Files.java:407)
    at htsjdk.samtools.seekablestream.SeekablePathStream.<init>(SeekablePathStream.java:39)
    at htsjdk.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:108)
    at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:252)
    ... 8 more
DavyCats commented 3 years ago

I'm not too familiar with this tool or its options, to be honest, but I suspect you need to give the sample name as noted in the VCF file, so: ./proband_bwaMEM_sort_dedupped.bam

And just as a heads up, this tool isn't really maintained anymore.