I am trying to do benchmarking for my pipeline (to analyze
germline and generate VCF file for
SNV and INDELs). to do so,
I got the WES data for this sample from hare:
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):
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?