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aseetharamaseetharam
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fixed bionano
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‎structural-variation/sv-calling.md

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```
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## 3. Calling variants using BioNano Solve
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Remove all the scaffolds from the genome (fasta file)
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```bash
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./separate-chr.sh <nam-genome>.fasta
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```
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Convert fasta to cmap format
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```
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fasta2cmap.sh <NAM-genome>-chr-only.fa
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```
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Call SV's against B73
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```
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bionano-call-SV.sh <NAM-genome>-chr-only.cmap
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```
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convert to vcf format
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```
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smap2vcf.sh
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```

‎structural-variation/sv-calling/bionano-call-SVs-enz1.sh

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#!/bin/bash
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source /work/LAS/mhufford-lab/arnstrm/miniconda3/etc/profile.d/conda.sh
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conda activate bionano
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#source activate bionano
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ml r-devtools/1.12.0-py2-r3.4-47jzlan
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ml rm perl
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ml rm python
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Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
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EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/bionano/Solve3.4_06042019a"
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rcmap="/work/LAS/mhufford-lab/arnstrm/stiff_stalks/Zea_mays_var_B73_V4_release/enz1/zm_B73_v4_all_chrs_un_ctgs-chr-only_CTTAAG_0kb_0labels.cmap"
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qcmap=$1
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python $EBROOTBIONANOSOLVE/Pipeline/06042019/runCharacterize.py \
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-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
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-r ${rcmap} \
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-q ${qcmap} \
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-p $EBROOTBIONANOSOLVE/Pipeline/06042019 \
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-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
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-n 32 > B73v4-${qcmap%.*}.stats
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python $EBROOTBIONANOSOLVE/Pipeline/06042019/runSV.py \
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-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
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-r ${rcmap} \
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-q ${qcmap} \
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-o B73v4-${qcmap%.*} \
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-E alignref/${qcmap%.*}.errbin \
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-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
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-j 32 \
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-T 32 \

‎structural-variation/sv-calling/bionano-call-SVs-enz2.sh

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#!/bin/bash
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source /work/LAS/mhufford-lab/arnstrm/miniconda3/etc/profile.d/conda.sh
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conda activate bionano
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#source activate bionano
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ml r-devtools/1.12.0-py2-r3.4-47jzlan
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ml rm perl
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ml rm python
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Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
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EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/bionano/Solve3.4_06042019a"
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rcmap="/work/LAS/mhufford-lab/arnstrm/stiff_stalks/Zea_mays_var_B73_V4_release/enz2/zm_B73_v4_all_chrs_un_ctgs-chr-only_GCTCTTC_0kb_0labels.cmap"
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qcmap=$1
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python $EBROOTBIONANOSOLVE/Pipeline/06042019/runCharacterize.py \
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-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
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-r ${rcmap} \
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-q ${qcmap} \
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-p $EBROOTBIONANOSOLVE/Pipeline/06042019 \
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-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
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-n 32 > B73v4-${qcmap%.*}.stats
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python $EBROOTBIONANOSOLVE/Pipeline/06042019/runSV.py \
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-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
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-r ${rcmap} \
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-q ${qcmap} \
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-o B73v4-${qcmap%.*} \
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-E alignref/${qcmap%.*}.errbin \
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-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
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-j 32 \
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-T 32 \

‎structural-variation/sv-calling/bionano-call-SVs.sh

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#!/bin/bash
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source /work/LAS/mhufford-lab/arnstrm/miniconda3/etc/profile.d/conda.sh
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conda activate bionano
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#source activate bionano
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ml r-devtools/1.12.0-py2-r3.4-47jzlan
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ml rm perl
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ml rm python
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Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
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EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/bionano/Solve3.4_06042019a"
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rcmap="/work/LAS/mhufford-lab/arnstrm/stiff_stalks/Zea_mays_var_B73_V4_release/zm_B73_v4_all_chrs_un_ctgs-chr-only_CTTAAG_CACGAG_0kb_0labels.cmap"
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qcmap=$1
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python $EBROOTBIONANOSOLVE/Pipeline/06042019/runCharacterize.py \
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-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
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-r ${rcmap} \
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-q ${qcmap} \
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-p $EBROOTBIONANOSOLVE/Pipeline/06042019 \
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-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
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-n 32 > B73v4-${qcmap%.*}.stats
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python $EBROOTBIONANOSOLVE/Pipeline/06042019/runSV.py \
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-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
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-r ${rcmap} \
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-q ${qcmap} \
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-o B73v4-${qcmap%.*} \
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-E alignref/${qcmap%.*}.errbin \
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-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
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-j 32 \
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-T 32 \

‎structural-variation/sv-calling/fasta2cmap.sh

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#!/bin/bash
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source /work/LAS/mhufford-lab/arnstrm/miniconda/etc/profile.d/conda.sh
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conda activate bionano
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ml r-devtools/1.12.0-py2-r3.4-47jzlan
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ml rm perl
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ml rm python
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Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
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EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/PanAnd/Solve3.4_06042019a"
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genome=$1
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perl $EBROOTBIONANOSOLVE/HybridScaffold/06042019/scripts/fa2cmap_multi_color.pl -i $genome -e CTTAAG 1 -e CACGAG 2

‎structural-variation/sv-calling/seprate-chr.sh

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#!/bin/bash
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genome=$1
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num=$(grep -n ">" $genome | head -n 11 |tail -n 1 |cut -f 1 -d ":" |awk '{print $1-1}' )
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head -n $num $genome > ${genome%.*}-chr-only.fa
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‎structural-variation/sv-calling/smap2vcf.sh

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#!/bin/bash
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source /work/LAS/mhufford-lab/arnstrm/miniconda3/etc/profile.d/conda.sh
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conda activate bionano
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ml r-devtools/1.12.0-py2-r3.4-47jzlan
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ml rm perl
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ml rm python
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Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
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EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/bionano/Solve3.4_06042019a"
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nam=$1
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#cd ${nam}/B73v5-*
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pwd
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python $EBROOTBIONANOSOLVE/VCFConverter/06042019/smap_to_vcf_v2.py \
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-s ${nam}.smap \
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-r ${nam}_r.cmap \
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-x ${nam}.xmap \
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-n ${nam} \
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-o ${nam} \
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-a "${nam}" \
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-b False

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