GTF to Refflat tool for use with CollectRnaSeqMetrics

Since most folks use GTFs for RNASeq, but CollectRnaSeqMetrics uses a refflat file, it would be nice to have a tool that can convert GTF to refflat, and then we can update CollectRnaSeqMetrics to take in either a refflat or GTF file.

This an example method (requires Jim Kent’s tools):

 gtfToGenePred \
    -genePredExt \
    -geneNameAsName2 \
    -ignoreGroupsWithoutExons \
    !{params.gtf} \
    /dev/stdout | \
    awk 'BEGIN { OFS="\t"} {print $12, $1, $2, $3, $4, $5, $6, $7, $8, $9, $10}' 

Also, it wouldn’t be hard to pull out the records with gene_type equal to rRNA to create the requisite ribosomal intervals.

[nh13]

@sooheelee yes, making CollectRnaSeqMetrics accept a refflat file would be great; I think I mentioned that above: “then we can update CollectRnaSeqMetrics to take in either a refflat or GTF file.” Nonetheless, if we are going to support a GTF as input to CollectRnaSeqMetrics, then 95% of the work would be done, and we could also have a really useful tool.

[sooheelee]

Why not just make CollectRnaSeqMetrics accept a GTF?