Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
Hello, I am currently working on optimizng a variant calling pipeline for short read RNA-Seq data, and i have been searching for any Gold Standard benchmarking datasets for the pipeline that has the VCF results provided and could not find any.
I know GIAB project provides Google-Illumina short read RNA-Seq datasets, but there is no curated VCF for the data that i can compare my final results with, so if anyone has an idea of what i can do it would be really helpful.
Thank you all in advance.
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As long as it is the same GIAB sample you could compare your SNP with the SNP's available for the whole genome set.
Thank you so much for answering! I actually found some studies doing it the way you mentioned.
I ran the GATK best practices pipeline on the RNA-Seq reads and compared it to the high confidence variants using hap.py, but the results do not make sense as it gave F1 Scores of about 0.04, which indicates i am doing something wrong in my analysis.
I tried every troubleshoot i could think of like checking my references, tools parameters, etc.., but could not grasp the cause of the problem, do you have any idea of what i could be doing wrong?