I tried to do what other posts reported and I have a problem that I do not fully understand why ...

1) I downloaded the fastq files from Garvan (ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/) with the bed file. I had to convert the bed file to hg38 (my_regions) ... as I understand it is in hg19.

2) I get the vcf (truth.vcf) and high confidence (confidence.bed) files from here ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/latest/GRCh38/

3) I ran the fastq files with the GATK codes, up to HaplotypeCaller. Garvan use 2 libraries for the same sample. I used them separately, I did not merg them at the end, before the variant calling.

4) To compere my query data (output of HaplotypeCaller) with the GIAB truth test I ran these two codes, to have also a .html file:

hap.py ${truth.vcf} ${query.vcf} -f ${confident} -o /hap.py_results/${outname} -r ${Hg38}

python rep.py -o /hap.py_results/"${outname}.html" "${outname}"_hap.py:/hap.py_results/"${outname}.roc.all.csv.gz"

5) I re-ran my results also with a similar code ... I found and tested it in a GA4GH tutorial:

hap.py ${truth.vcf} ${query.vcf} -f ${confident.bed} -o /hap.py_results/"${outname}" --engine=vcfeval --engine-vcfeval-path=rtg --no-decompose --no-leftshift

6) I ran also

rtg vcfeval -b ${truth.vcf} -c ${query.vcf} -o /hap.py_results/rtgHC/ -t ${ref_sdf} -e ${confidence.bed} --region=${my_regions}

Error: After applying regions there were no sequence names in common
between the reference and the supplied variant sets. Check the regions
supplied by --region or --bed-regions are correct.


chr1    826206  827522
chr1    827683  827775


confidence regions:

chr1    821881  822046
chr1    823126  823188
chr1    823426  823479
chr1    823580  826321
chr1    826481  827827
chr1    827928  839291



With the codes 5 and 6 the problem is that I have a recall of 1.65% ... the precision is 97.07% and the F-score is 0.033

What is the problem about "recall" and at the end with F-score? The intervals?
How can I fix the problem with the bed files? How they done the analysis considering that the intervals in the to bed files do not overlap?

Many thanks for your time!

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