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added -5SP to bwa mem
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lh3 committed Jul 27, 2018
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -5,7 +5,7 @@ curl -L https:// | tar -jxf -
cd hickit-0.1_x64-linux

# Map Dip-C reads and extract contacts (skip if you use your own pipeline)
./seqtk mergepe read1.fq.gz read2.fq.gz | ./pre-dip-c - | bwa mem -p hs37d5.fa - | gzip > aln.sam.gz
./seqtk mergepe read1.fq.gz read2.fq.gz | ./pre-dip-c - | bwa mem -5SP -p hs37d5.fa - | gzip > aln.sam.gz
./k8 hickit.js vcf2tsv phased.vcf > phased_SNP.tsv # extract phased SNPs from VCF
./k8 hickit.js sam2seg -v phased_SNP.tsv aln.sam.gz | ./k8 hickit.js chronly - | gzip > contacts.seg.gz
./hickit -i contacts.seg.gz -o - | bgzip > contacts.pairs.gz # optional
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