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GATK 184.108.40.206 GenomicsDBImport error : Duplicate field name AF found in vid attribute "fields"
Hello GATK team!
I am currently following your best practices for Mutect2 somatic calling. In the steps of creating a PoN, I got my normal samples' gVCF perfectly fine.
However, at the previous step of using
CreateSomaticPanelOfNormals, I need to use
This step is not working and I am running out of ideas.
This is the command I used :
gatk --java-options "-XX:+UseParallelGC -XX:ParallelGCThreads=4 -Xmx14g -Xms14g -Djava.io.tmpdir=/tmp/pon" GenomicsDBImport -R Homo_sapiens_assembly38.fasta -V 1.vcf.gz -V 2.vcf.gz -V 3.vcf.gz -V 4.vcf.gz -V 5.vcf.gz -V 6.vcf.gz -V 7.vcf.gz -V 8.vcf.gz -V 9.vcf.gz -V 10.vcf.gz -V 11.vcf.gz -V 12.vcf.gz -V 13.vcf.gz -V 14.vcf.gz -V 15.vcf.gz -V 16.vcf.gz -V 17.vcf.gz -V 18.vcf.gz -V 19.vcf.gz -V 20.vcf.gz -V 21.vcf.gz -V 22.vcf.gz -V 23.vcf.gz -V 24.vcf.gz -L wgs_calling_regions.hg38.interval_list --tmp-dir=/tmp/pon --genomicsdb-workspace-path pon_db
And the last lines of the log are :
... 16:04:31.323 INFO ProgressMeter - Starting traversal 16:04:31.323 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute 16:04:33.428 INFO GenomicsDBImport - Importing batch 1 with 24 samples Duplicate field name AF found in vid attribute "fields" terminate called after throwing an instance of 'FileBasedVidMapperException' what(): FileBasedVidMapperException : Duplicate fields exist in vid attribute "fields"
It is true, if I look for
AF occurences in one of the VCF header, I find :
$ zgrep "AF" 1.vcf.gz ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> ##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative-log-10 population allele frequencies of alt alleles">
What is the issue according to you?