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.

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2015-11-15
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