rna-test

rna_test.sh is a shell script to run GATK best practice for variant-calling in RNAseq. It uses STAR2.5 for alignment, HaplotypeCaller to call variants, and Annovar to annotate. It also employs STAR-Fusion, Cufflinks and Stringtie FPKM, HTSeq_count and BAM-readcount.

Notice:
STAR_gene_read and HTSeq_count are added.
exac03nontcga is added.
STAR-Fusion is added.
Stringtie is added.
Disable BQSR (-skb) opteion is added.
New avsnp(150) is updated.
use -dcov in SplitNCigarReads added.
Mutlithreading for dbsnp annotation, Haplotypecaller, and bamreadcount more efficient.
UMI function is added.
Allelic fraction is added.
Better COSMIC and CLINVAR annotation.
Arriba added.

Project Activity

See All Activity >

Follow rna-test

rna-test Web Site

Other Useful Business Software

Simple, Secure Domain Registration

Get your domain at wholesale price. Cloudflare offers simple, secure registration with no markups, plus free DNS, CDN, and SSL integration.

Register or renew your domain and pay only what we pay. No markups, hidden fees, or surprise add-ons. Choose from over 400 TLDs (.com, .ai, .dev). Every domain is integrated with Cloudflare's industry-leading DNS, CDN, and free SSL to make your site faster and more secure. Simple, secure, at-cost domain registration.

Rate This Project

User Reviews

Be the first to post a review of rna-test!

Additional Project Details

Registered

2015-11-15

Report inappropriate content