Clair3 GVCF created file is 1bp of the end sequence so validatevariants fails

[klausyboi]

Hi,

Im trying to combine my gvcfs, first using gatks validatevariants but i get the error:

A GVCF must cover the entire region. Found 16 loci with no VariantContext covering it. The first uncovered segment is:Pf3D7_01_v3:640851

Looking at a sample that worked from illumina the bp is always 1 short for each chromosome and 640851 is the end of the chromosome in this case so i think thats the problem.

I used clair3 to get the gvcf using:
barcode=$(basename "$barcode_dir")
run_clair3.sh \
--bam_fn=barcodes/$barcode/calls_"$barcode"sorted.bam \
--ref_fn=${ref_seq} \
--threads=${threads} \
--platform="ont" \
--model_path=/mnt/storageG1/data/software/rerio/clair3_models/r1041_e82${bps}_${type}_v500 \
--output=vcf/$barcode/ \
--include_all_ctgs \
--gvcf

I then used sortvcf from gatk because the variants were all in the wrong order and I was getting this error, hoping it would fix it but alas it did not.

Any help with this is greatly appreciated.

Thanks

[aquaskyline]

Could you please send over the reads and reference sequence of Pf3D7_01_v3. We will try the repeat the problem on our side.

[klausyboi]

ref genome
my bam
my fastq if you wanted to start from there which was created from the bam anyway but otherwise id be sending over lots of pod5s