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  • PileupBasedVariantCalling
    ...s tool at this point. If you have questions, please contact Hyun Min Kang (hmkang@umich.edu). % /net/fantasia/home/hmkang/bin/captTest/bin/capt-pileup
    7 KB (1,018 words) - 15:52, 10 September 2013
  • SeqShop: Genetic Association Analysis Practical, June 2014
    source /home/hmkang/seqshop/setup.txt export GC=/home/hmkang/seqshop/gotcloud
    19 KB (2,551 words) - 10:27, 2 February 2017
  • SeqShop: Association Analysis, May 2015
    /home/hmkang/seqshop/epacts/bin/anno -i /net/seqshop-server/hmkang/out/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.g /home/hmkang/seqshop/ref22/human_g1k_v37.chr22.fa -f refGene -g /home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz \
    20 KB (2,538 words) - 14:15, 21 May 2015
  • SeqShop: Genetic Association Analysis Practical, December 2014
    /home/hmkang/seqshop/epacts/bin/anno -i /net/seqshop-server/hmkang/out/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.g /home/hmkang/seqshop/ref22/human_g1k_v37.chr22.fa -f refGene -g /home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz \
    21 KB (2,694 words) - 10:27, 2 February 2017
  • SeqShop: Analysis of Structural Variation Practical, June 2014
    HG00641 ALL /net/seqshop-server/hmkang/out/bams/HG00641.recal.bam HG00640 ALL /net/seqshop-server/hmkang/out/bams/HG00640.recal.bam
    17 KB (2,452 words) - 14:37, 13 November 2014
  • SeqShop: Analysis of Structural Variation Practical, May 2015
    HG00641 /net/seqshop-server/home/hmkang/out/bams/HG00641.recal.bam HG00640 /net/seqshop-server/home/hmkang/out/bams/HG00640.recal.bam
    20 KB (2,783 words) - 15:56, 25 August 2015
  • VcfCooker
    ...Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
    9 KB (1,110 words) - 01:51, 31 October 2015
  • SeqShop: Analysis of Structural Variation Practical, December 2014
    HG00641 /net/seqshop-server/home/hmkang/out/bams/HG00641.recal.bam HG00640 /net/seqshop-server/home/hmkang/out/bams/HG00640.recal.bam
    21 KB (2,922 words) - 17:09, 17 December 2014
  • GotCloud: GenomeSTRiP Pipeline
    GENOMESTRIP_MASK_FASTA = /net/bipolar/hmkang/ref/hs37d5/genomeSTRiP/human_g1k_v37.mask.100.fasta GENOMESTRIP_PLOIDY_MAP = /net/bipolar/hmkang/2013_09/seqshop/reference/svtoolkit/conf/humgen_g1k_v37_ploidy.map
    14 KB (1,857 words) - 18:47, 10 February 2015
  • Sequence Analysis Practice 2011/03/09
    [[Media:Hmkang-20110309-practical.pdf | Low-level Processing - Practical Slides (PDF)]]
    6 KB (840 words) - 13:29, 10 March 2011
  • UMAKE
    ...Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
    16 KB (2,060 words) - 11:53, 2 February 2017
  • LiftOver
    * Hyun: provides sample liftOver tool: [/net/wonderland/home/hmkang/prj/Sardinia/MetaboChip/scripts/j01-liftover-metabochip-positions.pl]
    14 KB (2,263 words) - 18:33, 15 July 2015
  • TabAnno
    --tabix '/net/fantasia/home/hmkang/bin/annovar/humandb/hg19_ljb_all.txt.gz(chrom=1,pos=2,ref=4,alt=5,mySift=6,
    14 KB (1,969 words) - 11:57, 2 February 2017
  • SeqShop: Calling Your Own Genome, May 2015
    export HK=/net/seqshop-server/home/hmkang/apigenome/bin
    13 KB (2,110 words) - 12:10, 22 May 2015
  • EPACTS
    /net/fantasia/home/hmkang/tools/epacts-3.3.0/bin/epacts/ EPACTS_DIR=/net/fantasia/home/hmkang/tools/epacts-3.3.0/bin/epacts (in bash)
    41 KB (5,647 words) - 08:03, 19 February 2019
  • SeqShop: Calling Your Own Genome, December 2014
    export HK=/net/seqshop-server/home/hmkang/seqshop/bin
    18 KB (2,806 words) - 12:16, 15 December 2014
  • VerifyBamID
    ...ing, Goncalo Abecasis, and Michael Boehnke. Please email to Hyun Min Kang [hmkang@umich.edu ] for any questions.
    20 KB (2,795 words) - 15:29, 9 September 2017
  • EPACTS for DIAGRAM
    <pre>/net/fantasia/home/hmkang/sw/epacts2.1/</pre>
    24 KB (3,442 words) - 10:05, 2 February 2017
  • Tutorial: GotCloud UW CMG
    d-69-91-154-62:~ hmkang$ cat tmp.txt | perl -lane 's/test\.v1/test/g; print " $_"'
    46 KB (5,757 words) - 16:15, 6 August 2013
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