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vladimirsouza / lrRNAseqVariantCalling

Codes for the Iso-Seq variant-calling paper
MIT License
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Requesting the filtered ground-truth variants #5

Open huangnengCSU opened 8 months ago

huangnengCSU commented 8 months ago

Hi, Thanks for the useful variant calling tool for long-read RNA sequencing data. Since the entire tool and the evaluation process are developed in R language, it may be difficult for users who are not familiar with R language. Could you please release the ground-truth variants of WTC-11 dataset (filtered by short-read variant density and short-read coverage)? So that we don't have to download the huge short-read bam and run the time-consuming steps to calculate the bam's depth.

Best, Neng

vladimirsouza commented 4 months ago

Hi huangnengCSU,

Sorry for the late reply.

Our tool is built in R but you can run the entire pipeline using the terminal command line. See a tutorial here.

The ground-truth VCF file for WTC11 that we used in this work can be downloaded from the Allen Institute, as described in the Availability of data and materials section of our paper. Before using this VCF file as the ground-truth, we did some filtering on it, which we showed here.

huangnengCSU commented 4 months ago

Thanks. But could you share the filtered ground truth vcf file of WTC11 and jurkat on zenodo? This will make it easier to follow your work.