added griffin

griffin/runners/GC_correction.sh

@@ -0,0 +1,71 @@
+#!/bin/bash
+
+griffin=/cluster/projects/pughlab/bin/Griffin/v0.2.0
+basedir=/cluster/projects/pughlab/projects/CHARM/LFS/griffin2
+ref=/cluster/projects/pughlab/references/TGL/hg38/hg38_random.fa
+input=/cluster/projects/pughlab/external_data/TGL49_CHARM/LFS/LFS_WG/bams
+outdir=$basedir/output/GC_correction
+shdir=$basedir/sh_scripts/GC_correction
+
+mkdir -p $outdir
+mkdir -p $shdir
+mkdir -p $outdir/mappability_bias
+mkdir -p $outdir/mappability_plots
+mkdir -p $outdir/tmp
+
+cd $input
+ls *bam > $shdir/bams
+
+cd $shdir
+sed 's/....$//' bams > bam
+mv bam bams
+
+for bam in $(cat bams);do
+
+name=${bam:0:25}
+echo $bam
+echo $name
+
+mkdir -p $outdir/tmp/$name
+
+echo -e "#!/bin/bash
+source activate base
+conda activate griffin2" > $shdir/${name}.sh
+
+echo -e "$griffin/scripts/griffin_mappability_correction.py \
+--bam_file $input/${bam}.bam \
+--bam_file_name $name \
+--output $outdir/mappability_bias/${name}.mappability_bias.txt \
+--output_plot $outdir/mappability_plots/${name}.mappability_bias.pdf \
+--mappability $griffin/Ref/k50.Umap.MultiTrackMappability.hg38.bw \
+--exclude_paths $griffin/Ref/encode_unified_GRCh38_exclusion_list.bed \
+--chrom_sizes $griffin/Ref/hg38.standard.chrom.sizes \
+--map_quality 20 \
+--CPU 8 \
+--tmp_dir $outdir/tmp/$name" >> $shdir/${name}.sh
+
+echo -e "$griffin/scripts/griffin_GC_counts.py \
+--bam_file $input/${bam}.bam \
+--bam_file_name $name \
+--mappable_regions_path $griffin/Ref/k100_minus_exclusion_lists.mappable_regions.hg38.bed \
+--ref_seq $ref \
+--chrom_sizes $griffin/Ref/hg38.standard.chrom.sizes \
+--out_dir $outdir \
+--map_q 20 \
+--size_range 15 500 \
+--CPU 8" >> $shdir/${name}.sh
+
+echo -e "$griffin/scripts/griffin_GC_bias.py \
+--bam_file_name $name \
+--mappable_name k100_minus_exclusion_lists.mappable_regions.hg38 \
+--genome_GC_frequency $griffin/Ref/genome_GC_frequency \
+--out_dir $outdir/ \
+--size_range 15 500" >> $shdir/${name}.sh
+
+done
+
+cd $shdir
+ls *.sh > files
+for file in $(cat files);do
+sbatch -p all -c 8 --mem 8G -t 24:00:00 $file
+done

griffin/runners/nucleosome_profiling.sh

@@ -0,0 +1,107 @@
+#!/bin/bash
+
+analysis=hematopoetic
+CPU=1
+mem=8G
+
+griffin=/cluster/projects/pughlab/bin/Griffin/v0.2.0
+basedir=/cluster/projects/pughlab/projects/CHARM/LFS/griffin2
+sites=$griffin/site_configs/${analysis}_sites.yaml
+ref=/cluster/projects/pughlab/references/TGL/hg38/hg38_random.fa
+input=/cluster/projects/pughlab/external_data/TGL49_CHARM/LFS/LFS_WG/bams
+counts=$basedir/output/GC_correction
+outdir=$basedir/output/nucleosome_profiling/$analysis
+shdir=$basedir/sh_scripts/nucleosome_profiling/$analysis
+
+encode_exclude=$griffin/Ref/encode_unified_GRCh38_exclusion_list.bed
+centromere_path=$griffin/Ref/hg38_centromeres.bed
+gap_path=$griffin/Ref/hg38_gaps.bed
+patch_path=$griffin/Ref/hg38_fix_patches.bed
+alternative_haplotype_path=$griffin/Ref/hg38_alternative_haplotypes.bed
+
+mkdir -p $outdir
+mkdir -p $outdir/tmp
+mkdir -p $outdir/results
+mkdir -p $shdir
+
+cd $input
+ls *bam > $shdir/bams
+
+cd $shdir
+sed 's/....$//' bams > bam
+mv bam bams
+
+for bam in $(cat bams);do
+
+name=${bam:0:25}
+echo $bam
+echo $name
+
+echo -e "#!/bin/bash\n
+source activate base\n
+conda activate griffin2\n" > $shdir/${name}.sh
+
+echo -e "$griffin/scripts/griffin_coverage.py \
+--sample_name $name \
+--bam $input/${bam}.bam \
+--GC_bias $counts/GC_bias/${name}.GC_bias.txt \
+--mappability_bias $counts/mappability_bias/${name}.mappability_bias.txt \
+--mappability_correction True \
+--tmp_dir $outdir/tmp \
+--reference_genome $ref \
+--mappability_bw $griffin/Ref/k50.Umap.MultiTrackMappability.hg38.bw \
+--chrom_sizes_path $griffin/Ref/hg38.standard.chrom.sizes \
+--sites_yaml $sites \
+--griffin_scripts $griffin/scripts \
+--chrom_column Chrom \
+--position_column position \
+--strand_column Strand \
+--chroms chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 \
+--norm_window -5000 5000 \
+--size_range 100 200 \
+--map_quality 20 \
+--number_of_sites none \
+--sort_by none \
+--ascending none \
+--CPU $CPU\n" >> $shdir/${name}.sh
+
+echo -e "$griffin/scripts/griffin_merge_sites.py \
+--sample_name $name \
+--uncorrected_bw_path $outdir/tmp/$name/tmp_bigWig/${name}.uncorrected.bw \
+--GC_corrected_bw_path $outdir/tmp/$name/tmp_bigWig/${name}.GC_corrected.bw \
+--GC_map_corrected_bw_path $outdir/tmp/$name/tmp_bigWig/${name}.GC_map_corrected.bw \
+--mappability_correction False \
+--tmp_dir $outdir/tmp \
+--results_dir $outdir/results \
+--mappability_bw $griffin/Ref/k50.Umap.MultiTrackMappability.hg38.bw \
+--chrom_sizes_path $griffin/Ref/hg38.standard.chrom.sizes \
+--sites_yaml $sites \
+--griffin_scripts $griffin/scripts \
+--chrom_column Chrom \
+--position_column position \
+--strand_column Strand \
+--chroms chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 \
+--norm_window -5000 5000 \
+--save_window -1000 1000 \
+--fft_window -960 960 \
+--fft_index 10 \
+--smoothing_length 165 \
+--exclude_paths $encode_exclude $centromere_path $gap_path $patch_path $alternative_haplotype_path \
+--step 15 \
+--CNA_normalization False \
+--individual False \
+--smoothing True \
+--exclude_outliers True \
+--exclude_zero_mappability True \
+--number_of_sites none \
+--sort_by none \
+--ascending none \
+--CPU $CPU\n" >> $shdir/${name}.sh
+
+done
+
+cd $shdir
+ls *.sh > files
+for file in $(cat files);do
+sbatch -c $CPU --mem $mem -t 24:00:00 $file
+done