STARConsensus generate transformed GFF/GTF

alexdobin / STAR

RNA-seq aligner

MIT License

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STARConsensus generate transformed GFF/GTF #1349

Open NTNguyen13 opened 3 years ago

NTNguyen13 commented 3 years ago

Hi, I can generate genome from STARconsensus pipeline using this command

STAR \
--runThreadN 15 \
--runMode genomeGenerate \
--genomeDir $star_genome_outdir \
--genomeFastaFiles $ref_fasta \
--sjdbGTFfile $annotation_path \
--sjdbOverhang 150 \
--genomeTransformVCF $vcf_file \
--genomeTransformType Haploid

However, I also want to obtain the GTF file transformed by variants inserted in the VCF file for other analysis. How can I generate it? Thank you

alexdobin commented 3 years ago

Hi @NTNguyen13

there is no option for it at the moment, but it would be a useful feature indeed.

Cheers Alex

NTNguyen13 commented 3 years ago

thank you very much, I am looking forward to this feature.