Question: VCF evaluation using RTG.jar vcfeval
0
gravatar for Sara
9 weeks ago by
Sara110
Sara110 wrote:

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

snp • 181 views
ADD COMMENTlink modified 8 weeks ago by Len Trigg1.5k • written 9 weeks ago by Sara110

I would contact Len Trigg at RTG: https://www.realtimegenomics.com/products/rtg-tools

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Kevin Blighe65k

Hi Sara,

I am also benchmarking my pipeline using the same dataset as you have used. My question to you is, why you have selected project.NIST.hc.snps.indels.vcf as gold standard (Truth VCF) VCF and not HG001_*.vcf.gz (located at ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/latest/GRCh37/)?

-Akshay

ADD REPLYlink written 7 weeks ago by Akshay Zawar10

You might get answer to your problem in this thread: vcfeval Error: No sample name provided but calls is a multi-sample VCF

ADD REPLYlink written 7 weeks ago by Akshay Zawar10
1
gravatar for Len Trigg
8 weeks ago by
Len Trigg1.5k
New Zealand
Len Trigg1.5k wrote:

Just circling back here for anyone coming from the future :-)

The --sample flag can be used to specify which sample to select from the baseline or calls VCF in the case of multi-sample VCFs. Check the vcfeval user manual for more information.

ADD COMMENTlink written 8 weeks ago by Len Trigg1.5k
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