suwangbio/hint repository overview

HiNT A computational method for detecting copy number variations and translocations from Hi-C data

HiNT (Hi-C for copy Number variation and Translocation detection), a computational method to detect CNVs and Translocations from Hi-C data. HiNT has three main components: HiNT-PRE, HiNT-CNV, and HiNT-TL. HiNT-PRE preprocesses Hi-C data and computes the contact matrix, which stores contact frequencies between any two genomic loci; both HiNT-CNV and HiNT-TL starts with HI-C contact matrix, predicts copy number segments, and inter-chromosomal translocations, respectively

How to run:

$ docker pull suwangbio/hint

$ docker run -v /path/to/your/data/directory/:/d1/:rw suwangbio/hint hint

run HiNT interactively

$ docker run -it -v /path/to/your/data/directory/:/d1/:rw suwangbio/hint

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Useful options:

hint pre:

--pairtoolspath /miniconda3/bin/pairtools

--samtoolspath /miniconda3/bin/samtools

--coolerpath /miniconda3/bin/cooler

--juicerpath /usr/local/bin/juicer_tools.1.8.9_jcuda.0.8.jar

hint cnv:

--bicseq /usr/local/bin/BICseq2-seg_v0.7.3

hint tl:

--ppath /miniconda3/bin/pairix

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Example commands:

hint pre

$ hint pre -d /path/to/hic_1.fastq.gz,/path/to/hic_2.fastq.gz -i /path/to/bwaIndex/hg19/hg19.fa --refdir /path/to/refData/hg19 --informat fastq --outformat cooler -g hg19 -n test -o /path/to/outputdir --pairtoolspath /miniconda3/bin/pairtools --samtoolspath /miniconda3/bin/samtools --coolerpath /miniconda3/bin/cooler

$ hint pre -d /path/to/test.bam --refdir /path/to/refData/hg19 --informat bam --outformat juicer -g hg19 -n test -o /path/to/outputdir --pairtoolspath /miniconda3/bin/pairtools --samtoolspath /miniconda3/bin/samtools --juicerpath /usr/local/bin/juicer_tools.1.8.9_jcuda.0.8.jar

hin cnv

$ hint cnv -m contactMatrix.cool -f cooler --refdir /path/to/refDir/hg19 -r 50 -g hg19 -n test -o /path/to/outputDir --bicseq /usr/local/bin/BICseq2-seg_v0.7.3 -e MboI

$ hint cnv -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/50000 -f cooler --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /usr/local/bin/BICseq2-seg_v0.7.3 -e DpnII

$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /usr/local/bin/BICseq2-seg_v0.7.3 -e DpnII

hint tl

$ hint tl -m /path/to/data_1Mb.cool,/path/to/data_100kb.cool --chimeric /path/to/test_chimeric.sorted.pairsam.gz --refdir /path/to/refDir/hg19 --backdir /path/to/backgroundMatrices/hg19 --ppath /miniconda3/bin//pairix -f cooler -g hg19 -n test -o /path/to/outputDir

$ hint tl -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/1000000,/path/to/4DNFIS6HAUPP.mcool::/resolutions/100000 -f cooler --refdir /path/to/refDir/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /miniconda3/bin//pairix -p 12

$ hint tl -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refData/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /miniconda3/bin//pairix -p 12 -o HiNTtransl_juicerOUTPUT