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To Reproduce : I've ran truvari bench -b 00_ref/HG002_SVs_Tier1_v0.6.vcf.gz -c 06_sv/CD_3032_Cache.hg19.sv.vcf.gz -o 07_truvari/HG002_3032.truvari -f 00_ref/hg19.fa --includebed 00_ref/HG002_SVs_Tier1_v0.6.bed --passonly with and without the passonly tag and getting the same results.
I was successful in using HG002_GRCh38_CMRG_SV_v1.00.vcf.gz to test. So I'm not sure where the issue could be.
Additional details
Mapped the nanopore reads using minimap2 minimap2 -a -t 64 -x map-ont 00_ref/hg19.fa nanopore_reads.fastq.gz | samtools sort -@ 64 -O BAM --write-index -o nanopore_reads.sorted.bam -
Used sniffles2 to call SV: sniffles -i mapped_input.bam -v output.vcf.gz
The text was updated successfully, but these errors were encountered:
From the information provided my only assumption is that 06_sv/CD_3032_Cache.hg19.sv.vcf.gz is empty. The line 9655 chunks of 20041 variants Counter({'__filtered': 10400, 'base': 9641}) says that there are 20041 variants analyzed and the line Zipped 20041 variants Counter({'base': 20041}) says that all the variants are in the baseline vcf. If there were comparison variants, the lines would say something like Counter({'comp': 12345....
It's definitely not empty. I figured it out. It turns out I was using the wrong reference, that is, I was using hg19 from UCSC. I used the one from the NIST website directly and everything worked.
Version : v4.2.2
Describe the bug :
I'm trying to benchmark Nanopore reads against the NIST v0.6 Tier 1 truth set but I'm getting the following error:
To Reproduce : I've ran
truvari bench -b 00_ref/HG002_SVs_Tier1_v0.6.vcf.gz -c 06_sv/CD_3032_Cache.hg19.sv.vcf.gz -o 07_truvari/HG002_3032.truvari -f 00_ref/hg19.fa --includebed 00_ref/HG002_SVs_Tier1_v0.6.bed --passonly
with and without thepassonly
tag and getting the same results.I was successful in using
HG002_GRCh38_CMRG_SV_v1.00.vcf.gz
to test. So I'm not sure where the issue could be.Additional details
minimap2 -a -t 64 -x map-ont 00_ref/hg19.fa nanopore_reads.fastq.gz | samtools sort -@ 64 -O BAM --write-index -o nanopore_reads.sorted.bam -
sniffles -i mapped_input.bam -v output.vcf.gz
The text was updated successfully, but these errors were encountered: