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4_LinkageDisequilibrium.md

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Linkage Disequilibrium

Data preparation

Download the files:

mkdir -p ../linkage_disequilibrium
cd ../linkage_disequilibrium

wget http://hypervolu.me/~guarracino/chrcommunity/chrACRO+refs.pq_contigs.1kbps.hg002prox.hg002hifi.fa.gz.7ef1ba2.04f1c29.ebc49e1.smooth.final.chm13.haploid.snv.norm.no_HG002-hifi.vcf.gz
wget http://hypervolu.me/~guarracino/chrcommunity/chrACRO_7-Dec-22_PHRs.bed
sed -i 's/^/chm13#/g' chrACRO_7-Dec-22_PHRs.bed

Remove CONFLICT regions from the VCF file:

zgrep -v "CONFLICT" chrACRO+refs.pq_contigs.1kbps.hg002prox.hg002hifi.fa.gz.7ef1ba2.04f1c29.ebc49e1.smooth.final.chm13.haploid.snv.norm.no_HG002-hifi.vcf.gz | \
    bgzip -c -@ 48 > chrACRO+refs.vcf.gz
tabix -p vcf chrACRO+refs.vcf.gz -f

Data exploration

Determine fraction onf missing sites per locus

mkdir stats 

plink \
--vcf chrACRO+refs.vcf.gz \
--missing  \
--chr-set -5 \
--allow-extra-chr \
--extract 'range' ../data/annotation/chm13.p_arms.approximate.acros.bed \
--out stats/chrACRO+refs.pArm 

plink \
--vcf chrACRO+refs.vcf.gz \
--missing  \
--chr-set -5 \
--allow-extra-chr \
--extract 'range' ../data/annotation/chm13.q_arms.approximate.acros.bed \
--out stats/chrACRO+refs.qArm 

plink \
--vcf chrACRO+refs.vcf.gz \
--chr-set -5 \
--missing  \
--allow-extra-chr \
--extract 'range' chrACRO_7-Dec-22_PHRs.bed \
--out stats/chrACRO+refs.PHR

Calculate allele frequencies

plink \
--vcf chrACRO+refs.vcf.gz \
--freq  \
--chr-set -5 \
--allow-extra-chr \
--out stats/chrACRO+refs

Make a file of chr positions

zcat chrACRO+refs.vcf.gz | grep -v '##' | cut -f1,2 > stats/chrpos.txt

visualization - supplementary figure

Rscript ../scripts/plot_stats.R 'stats/*.lmiss' 'stats/chrACRO+refs.frq' 'chrACRO_7-Dec-22_PHRs.bed' 'stats/chrpos.txt'  statsSupp.pdf

Compute linkage disequilibrium (LD)

Prepare files:

cat ../data/annotation/chm13.p_arms.approximate.acros.bed | cut -f 1 > chrNames.txt
cat ../data/annotation/chm13.p_arms.approximate.acros.bed | cut -f 1 | sed 's/chm13#//g' > acrocentrics.txt

Compute LD:

mkdir ld

winSize=70 # size of the window in kb 

# p arm
paste -d'\n' chrNames.txt acrocentrics.txt | while read f1 && read f2 ; do
  plink \
    --vcf chrACRO+refs.vcf.gz \
    --allow-extra-chr \
    --chr-set -5 \
    --chr $f1 \
    --r2 \
    --extract 'range' ../data/annotation/chm13.p_arms.approximate.acros.bed \
    --ld-window-kb $winSize --ld-window-r2 0 \
    --out ld/$f2.pArm;
done

# q arm
paste -d'\n' chrNames.txt acrocentrics.txt | while read f1 && read f2 ; do
  plink \
    --vcf chrACRO+refs.vcf.gz \
    --allow-extra-chr \
    --chr-set -5 \
    --chr $f1 \
    --r2 \
    --extract 'range' ../data/annotation/chm13.q_arms.approximate.acros.bed \
    --ld-window-kb $winSize --ld-window-r2 0\
    --out ld/$f2.qArm;
done

# putative recombinant
paste -d'\n' chrNames.txt acrocentrics.txt | while read f1 && read f2 ; do\
  plink \
    --vcf chrACRO+refs.vcf.gz \
    --allow-extra-chr \
    --chr-set -5 \
    --chr $f1 \
    --r2 \
    --extract 'range' chrACRO_7-Dec-22_PHRs.bed \
    --ld-window-kb $winSize --ld-window-r2 0 \
    --out ld/$f2.PHR;
done

Visualization

Rscript ../scripts/plot_ld_1.R 'ld/*.ld' 100 4000 ExtendedDataFigure11.pdf