Difference between revisions of "RV-TDT Exercise"
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| − | ==RV-TDT | + | ==RV-TDT exercise== |
| − | vtools init rvtdt | + | |
| + | vtools init rvtdt | ||
| + | vtools import --format vcf data/data.vcf --build hg19 | ||
| + | vtools phenotype --from_file data/phen.txt | ||
| + | # variant selection | ||
| + | vtools execute ANNOVAR geneanno | ||
| + | vtools select variant "variant.region_type like '%splicing%'or variant.mut_type like 'nonsynonymous%' or variant.mut_type like 'frameshift%' or variant.mut_type like 'stop%'" -t func_variant | ||
| + | # tped file | ||
| + | vtools export func_variant --format tped --samples 'phenotype is not null' > vat_raw.tped | ||
| + | sort -k4 -n vat_raw.tped | awk 'BEGIN{OFS="\t";prev="None";copy=1} {$2=$1"_"$4; $3=0; if($2==prev) {$2=$2"_"copy; copy=copy+1} else {prev=$2; copy=1}; print $0}' > vat_export.tped | ||
| + | # tfam file | ||
| + | vtools phenotype --out family sample_name pid mid sex phenotype > vat_export.tfam | ||
| + | # anno file | ||
| + | vtools use refGene-hg19_20130904 | ||
| + | vtools update func_variant --set 'maf=0.001' | ||
| + | vtools select func_variant -o chr pos refGene.name2 maf --header > vat_export.anno | ||
| + | # Mendelian error and recode | ||
| + | plink --noweb --tfile vat_export --me 1 1 --set-me-missing --make-bed --out "noME" | ||
| + | plink --bfile noME --recode12 --out "recode12_noME" | ||
| + | sort -n -k1 -k6 -k2 recode12_noME.ped | sed 's/ /\t/g' | cut -f1,3,4,5 --complement > linkage.ped | ||
| + | cut -f2 recode12_noME.map | awk 'BEGIN{OFS="\t";} {print "M",$0}' | sed '1i\I\tid\nA\tDisease' > linkage.dat | ||
| + | java -Xmx10000m -jar java/linkage2beagle.jar linkage.dat linkage.ped > pre_beagle.bgl | ||
| + | python script/pre_phase.py -i pre_beagle.bgl -a pre_beagle_withMissing.bgl | ||
| + | java -Xmx10000m -jar java/beagle.jar missing=0 trios=pre_beagle.bgl out=bgl_phased verbose=false redundant=true | ||
| + | gunzip bgl_phased.pre_beagle.bgl.phased.gz | ||
| + | python script/post_phase.py -a vat_export.anno -b bgl_phased.pre_beagle.bgl.phased -o genes/ | ||
| + | for g in `ls genes | grep tped | cut -d"." -f1 | head -20` | ||
| + | do | ||
| + | echo "runing rvTDT on gene "${g} | ||
| + | rvTDT exercise_proj -G ./genes/${g}.tped -P ./data/rvtdt.phen -M ./genes/${g}.map --adapt 500 --alpha 0.00001 --permut 2000 --lower_cutoff 0 --upper_cutoff 100 --minVariants 3 --maxMissRatio 1 | ||
| + | done | ||
| + | # Answer | ||
| + | vtools show tables | ||
| + | ls genes/ | grep tped | wc | ||
| + | cat exercise_proj_pval/*.pval | grep -v "^#" | sort -k2 | ||
| + | cat exercise_proj_pval/*.pval | grep -v "^#" | sort -k3 | ||
| + | # clean | ||
| + | rm -r exercise_proj* genes/* bgl* linkage* recode12* pre_beagle* vat_export.* | ||
Latest revision as of 17:42, 24 January 2019
RV-TDT exercise
vtools init rvtdt
vtools import --format vcf data/data.vcf --build hg19
vtools phenotype --from_file data/phen.txt
# variant selection
vtools execute ANNOVAR geneanno
vtools select variant "variant.region_type like '%splicing%'or variant.mut_type like 'nonsynonymous%' or variant.mut_type like 'frameshift%' or variant.mut_type like 'stop%'" -t func_variant
# tped file
vtools export func_variant --format tped --samples 'phenotype is not null' > vat_raw.tped
sort -k4 -n vat_raw.tped | awk 'BEGIN{OFS="\t";prev="None";copy=1} {$2=$1"_"$4; $3=0; if($2==prev) {$2=$2"_"copy; copy=copy+1} else {prev=$2; copy=1}; print $0}' > vat_export.tped
# tfam file
vtools phenotype --out family sample_name pid mid sex phenotype > vat_export.tfam
# anno file
vtools use refGene-hg19_20130904
vtools update func_variant --set 'maf=0.001'
vtools select func_variant -o chr pos refGene.name2 maf --header > vat_export.anno
# Mendelian error and recode
plink --noweb --tfile vat_export --me 1 1 --set-me-missing --make-bed --out "noME"
plink --bfile noME --recode12 --out "recode12_noME"
sort -n -k1 -k6 -k2 recode12_noME.ped | sed 's/ /\t/g' | cut -f1,3,4,5 --complement > linkage.ped
cut -f2 recode12_noME.map | awk 'BEGIN{OFS="\t";} {print "M",$0}' | sed '1i\I\tid\nA\tDisease' > linkage.dat
java -Xmx10000m -jar java/linkage2beagle.jar linkage.dat linkage.ped > pre_beagle.bgl
python script/pre_phase.py -i pre_beagle.bgl -a pre_beagle_withMissing.bgl
java -Xmx10000m -jar java/beagle.jar missing=0 trios=pre_beagle.bgl out=bgl_phased verbose=false redundant=true
gunzip bgl_phased.pre_beagle.bgl.phased.gz
python script/post_phase.py -a vat_export.anno -b bgl_phased.pre_beagle.bgl.phased -o genes/
for g in `ls genes | grep tped | cut -d"." -f1 | head -20`
do
echo "runing rvTDT on gene "${g}
rvTDT exercise_proj -G ./genes/${g}.tped -P ./data/rvtdt.phen -M ./genes/${g}.map --adapt 500 --alpha 0.00001 --permut 2000 --lower_cutoff 0 --upper_cutoff 100 --minVariants 3 --maxMissRatio 1
done
# Answer
vtools show tables
ls genes/ | grep tped | wc
cat exercise_proj_pval/*.pval | grep -v "^#" | sort -k2
cat exercise_proj_pval/*.pval | grep -v "^#" | sort -k3
# clean
rm -r exercise_proj* genes/* bgl* linkage* recode12* pre_beagle* vat_export.*
