I had to redo the calling of two of my samples, and now I am trying to redo my genomic database in order to replace these two samples.
module load gatk/126.96.36.199
gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport --genomicsdb-workspace-path gDB5b --batch-size 215 --sample-name-map allgvcflist.txt --reader-threads 4 -L chr5
A USER ERROR has occurred: Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception: java.lang.NumberFormatException: For input string: "0/0:28:72:28:0,72,942"
I run ValidateVariants and it doesn’t give any errors:
gatk ValidateVariants -R /.../ucsc.hg19.fasta -V /.../A881.g.vcf --dbsnp dbsnp_138.hg19.vcf --validation-type-to-exclude ALL
Why is it giving this error and how can I solve it?
Thank you for any help
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