Hi, I am running hap.py with vcfeval on GIAB high conf vcf file. However, I am getting 0 counts for all the metrics in the comparison result. I have corrected my files for the chromosome naming convention (chr). However, still, I am getting this issue. Any help on this would be highly appreciated! Here is my command-
Hi, I am running hap.py with vcfeval on GIAB high conf vcf file. However, I am getting 0 counts for all the metrics in the comparison result. I have corrected my files for the chromosome naming convention (chr). However, still, I am getting this issue. Any help on this would be highly appreciated! Here is my command-
~/hap.py-install/bin/hap.py /mnt/g/NGS_Pipeline/HG001_Fixchr.vcf.gz /mnt/g/NGS_Pipeline/BWA_MEM_Samtools_Pipeline/NIST7035_NA12878_sorted_rmdup.vcf.gz -f /mnt/g/NGS_Pipeline/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel.bed -r /mnt/g/NGS_Pipeline/GRCh37.p13.genome.fasta -o /mnt/g/NGS_Pipeline/Benchmarking/test --engine=vcfeval --engine-vcfeval-path /mnt/g/NGS_Pipeline/RTGvcfeval/rtg-tools/dist/rtg-tools-3.11-39691f9f/rtg --fixchr --engine-vcfeval-template /mnt/g/NGS_Pipeline/GRCh37.p13.genome.sdf --verbose --logfile log.txt