gatk-workflows/gatk3-4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools

gatk3-4-rnaseq-germline-snps-indels's Issues

Question: mouse reference docs?

Hi,

Just curious, I'm new to variant calling and I'm not so familiar with some of the references (e.g. vcfindicies) or the specific index preparation preferred by GATK. The pipeline is extremely useful but it only points to a reference for human genomes. Is there somewhere mouse genomes are stored?

Thank you

gtf reference file

GTF reference file compatible with the references from the bundle should be provided. Here it looks like there's a "test" file that isn't available to the public

Quantifying the expression of SNVS & RNA-seq reads

Sorry,

This is not any issue with GATK indeed, rather my confusion;

I have been given a bunch of .bam files (marked duplicates) from STAR aligner; Likely I will need "Calling variants in RNAseq"

Sorry, please say I should find Reads overlapping any SNV using the ReadCountWalker in gatktools

I can not find any tutorial, related discussion, ..

Any help please? For workflow, getting intuition

Thank you, I look forward to hearing from you

Annotation file for RNA-seq variant calling

Hi,
I am trying to follow your workflow for RNA-seq variant calling but I am having trouble building the STAR index. I am using the HG38 fasta found here :
ftp://[email protected]/bundle/hg38/Homo_sapiens_assembly38.fasta.gz
But there is no associated annotation file. All the annotation files I have tried so far give an error at the end of the STAR indexing process.
There is an annotation file referenced in the file:
rna-germline-variant-calling.inputs.json
("RNAseq.annotationsGTF": "gs://gatk-test-data/intervals/star.gencode.v19.transcripts.patched_contigs.gtf",)
Would it be possible to upload this to the GATK resource pack? Or give me a link to somewhere that I can download it?
Thanks