First of, pardon my dual post of the same on GATK and here. I understand that GATK guys may not answer this in time also provided this is on a sat night and I am in super time crunch to get some evaluation metrics by monday and hence in a desperation I am seeking help here as well. So my apologies of the bat!
So here I go ...... I am running evaluate variants and encountered this error:
Now I would like to point out that I had the same error my first pass (ran until chr14 only) around and I looked for a solution on GATK forum. I had seen another post on GATK forum with the same error and that person had NOT sorted their vcf file, which is exactly what I had done/not done - not sorted vcf file.So I went back and sorted my input vcf file using picard tool and then fed my sorted file into evaluate variant command as shown below: It ran further more until chrX but then spit out this error below(ERROR).
One thing to point out is my sorted vcf has only few chromosomes I wanted to look at chr2,3,5,7 and 14. Is that an issue? I dont see how, but worth asking. Also is this a bug as I am running the BETA ?
Any help would be appreciated !! Pressed for time !!! Thankyou in advance!!!
gatk VariantEval -R Homo_sapiens_assembly38.fasta -eval fgeno_output_sorted.vcf -O fgeno_variant_eval.tbl -D dbsnp_146.hg38.vcf.gz -no-ev -EV CompOverlap -EV CountVariants -EV IndelSummary -EV MultiallelicSummary -EV TiTvVariantEvaluator
Why am I getting this error even though my file is sorted?
22:42:07.179 INFO ProgressMeter - chrX:124684150 39.6 147787000 3736018.7
22:42:17.192 INFO ProgressMeter - chrX:146492652 39.7 148520000 3738775.7
22:42:26.416 INFO VariantEval - Shutting down engine
[August 15, 2020 10:42:26 PM EDT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 39.91 minutes.
java.lang.IllegalStateException: The elements of the input Iterators are not sorted according to the comparator htsjdk.variant.variantcontext.VariantContextComparator