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Showing 2 open source projects for "bam readcount"

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    rna-test

    script for variant calling of RNA-Seq

    ...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. ...
    Downloads: 0 This Week
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  • 2

    exome-test

    script for variant calling of Exome-Seq

    exome_test.sh is a shell script to run GATK best practice and varscan for variant-calling in exomseq. It uses bwa for alignment, UnifiedGenotyper and varscan to call variants, and Annovar to annotate. It also employs DepthofCoverage and BAM-readcount. [Notice] MAF files compatible with MutSigCV are added. The Annovar filter dbnsfp30a is updated. Correction of an error in the title line of merge file. -ni option added. -vb option (-B in varscan) added exac03nontcga is added. An error about VARSCAN is corrected. Mutlithreading for dbsnp annotation, Haplotypecaller, Varscan and bamreadcount more efficient. ...
    Downloads: 0 This Week
    Last Update:
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