gatk Funcotator

Question

[Saurabh]

Hello!

I'm getting an error like this

A USER ERROR has occurred: Cannot read file://file.vcf because no suitable codecs found

while running gatk funcotator. Can anyone guide me how do I solve the error?

Thanks!

Used command:

java -jar gatk Funcotator -V file.vcf --ref-version hg19 -R ref_all.fasta --data-sources-path funcotator_dataSources.v1.6.20190124s --output-file-format VCF -O out.vcf.gz

[Pierre Lindenbaum]

what is the output of

$ file file.vcf

?

[Saurabh]

Output:

##fileformat="VCFv4.2"                          
##fileDate="2023-06-21"                         
##source="UMI-VarCal"                           
##toolVersion="2.6.0"                           
##command="input='/scratch/duttlab/Bhargavi/Liquid_biopsy_LUAD/Saurabh/TCS005_S15_fxd_sorted.bam', bed='/scratch/duttlab/Bhargavi/Liquid_biopsy_LUAD/Saurabh/A3416642_AllTracks.bed', fasta='/scratch/duttlab/database/human_reference_genome_hg19/hg19_all.fasta', out='/scratch/duttlab/Bhargavi/Liquid_biopsy_LUAD/Saurabh/out2', min_base_quality=10, min_read_quality=20, min_mapping_quality=20, min_variant_umi=5, strand_bias_method='default', max_strand_bias=1.0, alpha=0.05, max_hp_length=10, cores=3"                         
##reference="/scratch/duttlab/database/human_reference_genome_hg19/hg19_all.fasta"                          
##FILTER=<ID=ID,Description="Generic filter">                           
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele frequency based on allele count/depth">                           
##INFO=<ID=UMI_AF,Number=2,Type=Float,Description="Allele frequency based on UMI count/depth">                          
##INFO=<ID=AO,Number=3,Type=Integer,Description="Alternate allele observation count">                           
##INFO=<ID=DP,Number=4,Type=Integer,Description="Total read depth at the locus">                            
##INFO=<ID=HP,Number=5,Type=Integer,Description="Homopolymer length at the locus">                          
##INFO=<ID=TYPE,Number=6,Type=String,Description="The variation type: either SNV, INS or DEL">                          
##INFO=<ID=CONF,Number=7,Type=String,Description="Confidence of the variant. It has 5 levels: low(1/5), average(2/5), high(3/5), strong(4/5) or certain(5)">                            
##INFO=<ID=PHASED,Number=8,Type=List(String),Description="List of phased variants">                         
##INFO=<ID=PHASED_UMI,Number=9,Type=List(Integer),Description="List of the number of common UMI with every phased variant">                         
##INFO=<ID=PHASED_VAF_RATIO,Number=10,Type=List(Float),Description="List of the VAF Ratio  with every phased variant">                          
#CHROM  POS ID  REF ALT Q-VALUE FILTER  INFO
chr1    204460681   chr1:204460681T>C   T   C   0   PASS    AF=1.0;UMI_AF=1.0;AO=10;DP=10;HP=1;TYPE=SNV;CONF=STRONG;PHASED=NA;PHASED_UMI=NA;PHASED_VAF_RATIO=NA
chr2    84036   chr2:84036CT>C  CT  C   2.10E-10    PASS    AF=0.003;UMI_AF=0.003;AO=12;DP=3722;HP=8;TYPE=DEL;CONF=AVERAGE;PHASED=NA;PHASED_UMI=NA;PHASED_VAF_RATIO=NA

.. .. and list goes on

[Pierre Lindenbaum]

it cannot be the output of the 'file' command.

[Pierre Lindenbaum]

try to use a compressed + indexed vcf.gz input instead of a plain vcf

[Saurabh]

getting an error like this: index: "file.vcf.gz" is in a format that cannot be usefully indexed

[Saurabh]

how do I resolve?

[Pierre Lindenbaum]

vcf file must be compressed with a bgzip compressor, not just gzip

bcftools view -O z -o file.vcf.gz file.vcf && bcftools index -t -f file.vcf.gz

[Saurabh]

whats z denotes in code?

[Pierre Lindenbaum]

https://samtools.github.io/bcftools/bcftools.html#common_options

[Saurabh]

Failed to read from file.vcf: unknown file type

[Pierre Lindenbaum]

this is not a vcf file. it has never been a vcf file. see gatk Funcotator

[Saurabh]

what do I've to do? can you give me suggestion. Thanks!