fixed bionano

structural-variation/sv-calling.md

@@ -131,3 +131,29 @@ cd r2_vcf
 ```
 
 ## 3. Calling variants using BioNano Solve
+
+
+Remove all the scaffolds from the genome (fasta file)
+
+```bash
+./separate-chr.sh <nam-genome>.fasta
+```
+
+Convert fasta to cmap format
+
+
+```
+fasta2cmap.sh <NAM-genome>-chr-only.fa
+```
+
+Call SV's against B73
+
+```
+bionano-call-SV.sh <NAM-genome>-chr-only.cmap
+```
+
+convert to vcf format
+
+```
+smap2vcf.sh
+```

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

@@ -0,0 +1,28 @@
+#!/bin/bash
+source /work/LAS/mhufford-lab/arnstrm/miniconda3/etc/profile.d/conda.sh
+conda activate bionano
+#source activate bionano
+ml r-devtools/1.12.0-py2-r3.4-47jzlan
+ml rm perl
+ml rm python
+Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
+EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/bionano/Solve3.4_06042019a"
+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"
+qcmap=$1
+python $EBROOTBIONANOSOLVE/Pipeline/06042019/runCharacterize.py \
+-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
+-r ${rcmap} \
+-q ${qcmap} \
+-p $EBROOTBIONANOSOLVE/Pipeline/06042019 \
+-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
+-n 32 > B73v4-${qcmap%.*}.stats
+
+python $EBROOTBIONANOSOLVE/Pipeline/06042019/runSV.py \
+-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
+-r ${rcmap} \
+-q ${qcmap} \
+-o B73v4-${qcmap%.*} \
+-E alignref/${qcmap%.*}.errbin \
+-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
+-j 32 \
+-T 32 \

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

@@ -0,0 +1,28 @@
+#!/bin/bash
+source /work/LAS/mhufford-lab/arnstrm/miniconda3/etc/profile.d/conda.sh
+conda activate bionano
+#source activate bionano
+ml r-devtools/1.12.0-py2-r3.4-47jzlan
+ml rm perl
+ml rm python
+Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
+EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/bionano/Solve3.4_06042019a"
+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"
+qcmap=$1
+python $EBROOTBIONANOSOLVE/Pipeline/06042019/runCharacterize.py \
+-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
+-r ${rcmap} \
+-q ${qcmap} \
+-p $EBROOTBIONANOSOLVE/Pipeline/06042019 \
+-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
+-n 32 > B73v4-${qcmap%.*}.stats
+
+python $EBROOTBIONANOSOLVE/Pipeline/06042019/runSV.py \
+-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
+-r ${rcmap} \
+-q ${qcmap} \
+-o B73v4-${qcmap%.*} \
+-E alignref/${qcmap%.*}.errbin \
+-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
+-j 32 \
+-T 32 \

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

@@ -0,0 +1,28 @@
+#!/bin/bash
+source /work/LAS/mhufford-lab/arnstrm/miniconda3/etc/profile.d/conda.sh
+conda activate bionano
+#source activate bionano
+ml r-devtools/1.12.0-py2-r3.4-47jzlan
+ml rm perl
+ml rm python
+Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
+EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/bionano/Solve3.4_06042019a"
+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"
+qcmap=$1
+python $EBROOTBIONANOSOLVE/Pipeline/06042019/runCharacterize.py \
+-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
+-r ${rcmap} \
+-q ${qcmap} \
+-p $EBROOTBIONANOSOLVE/Pipeline/06042019 \
+-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
+-n 32 > B73v4-${qcmap%.*}.stats
+
+python $EBROOTBIONANOSOLVE/Pipeline/06042019/runSV.py \
+-t $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/RefAligner \
+-r ${rcmap} \
+-q ${qcmap} \
+-o B73v4-${qcmap%.*} \
+-E alignref/${qcmap%.*}.errbin \
+-a $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel/optArguments_nonhaplotype_noES_DLE1_saphyr.xml \
+-j 32 \
+-T 32 \

structural-variation/sv-calling/fasta2cmap.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+source /work/LAS/mhufford-lab/arnstrm/miniconda/etc/profile.d/conda.sh
+conda activate bionano
+ml r-devtools/1.12.0-py2-r3.4-47jzlan
+ml rm perl
+ml rm python
+Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
+EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/PanAnd/Solve3.4_06042019a"
+genome=$1
+perl $EBROOTBIONANOSOLVE/HybridScaffold/06042019/scripts/fa2cmap_multi_color.pl -i $genome -e CTTAAG 1 -e CACGAG 2

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

@@ -0,0 +1,5 @@
+#!/bin/bash
+genome=$1
+num=$(grep -n ">" $genome | head -n 11 |tail -n 1 |cut -f 1 -d ":" |awk '{print $1-1}' )
+head -n $num $genome > ${genome%.*}-chr-only.fa
+

structural-variation/sv-calling/smap2vcf.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+source /work/LAS/mhufford-lab/arnstrm/miniconda3/etc/profile.d/conda.sh
+conda activate bionano
+ml r-devtools/1.12.0-py2-r3.4-47jzlan
+ml rm perl
+ml rm python
+Rscript -e '.libPaths("~/R/x86_64-pc-linux-gnu-library/3.4/")'
+EBROOTBIONANOSOLVE="/work/LAS/mhufford-lab/arnstrm/bionano/Solve3.4_06042019a"
+nam=$1
+#cd ${nam}/B73v5-*
+pwd
+
+python $EBROOTBIONANOSOLVE/VCFConverter/06042019/smap_to_vcf_v2.py \
+-s ${nam}.smap \
+-r ${nam}_r.cmap \
+-x ${nam}.xmap \
+-n ${nam} \
+-o ${nam} \
+-a "${nam}" \
+-b False