Hi there,

I am trying to do benchmarking for my pipeline (to analyze WES and WGS germline and generate VCF file for SNV and INDELs). to do so,

I got the WES data for this sample from hare:

https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/

and worked on these 2 datasets separately:

NIST7035_TAAGGCGA_L001_R1_001_trimmed.fastq.gz
NIST7035_TAAGGCGA_L001_R2_001_trimmed.fastq.gz





NIST7086_CGTACTAG_L002_R1_001_trimmed.fastq.gz
NIST7086_CGTACTAG_L002_R2_001_trimmed.fastq.gz

and also the VCF file from the same link as my reference (golden standard):

project.NIST.hc.snps.indels.vcf

then I tried to use the following command to evaluate my VCF file(made for the above files using my pipeline):

java -Xmx4G -jar  RTG.jar vcfeval -t Homo_sapiens.GRCh37.GATK.illumina.SDF  -T 6 --baseline=[GIAB truth VCF] --calls=[SNV/INDEL VCF] --all-records --bed-regions=[Exome BED file]

I made this folder : Homo_sapiens.GRCh37.GATK.illumina.SDF using this command:

rtg format --output  Homo_sapiens.GRCh37.GATK.illumina.SDF  hg19.fasta

as --baseline I used above VCF file (the golden standardnd as --calls I used the VCF file that I made). I also got the bed file from the same link. when I run the RTG.jar using the mentioned command I would get this error:

Error: No sample name provided but baseline is a multi-sample VCF.

do you know how to fix the problem?

Thanks