RV-TDT Exercise - Revision history

Serveradmin at 17:42, 24 January 2019

2019-01-24T17:42:34Z

Serveradmin: /* RV-TDT exercise */

2017-03-08T18:40:03Z

‎RV-TDT exercise

Serveradmin: /* RV-TDT Exercise */

2017-02-23T17:40:31Z

‎RV-TDT Exercise

Serveradmin at 17:39, 23 February 2017

2017-02-23T17:39:43Z

Serveradmin: Created page with "__NO_TITLE__ ==RV-TDT Exercise== vtools init rvtdt
vtools import --format vcf data/data.vcf --build hg19
vtools phenotype --from_file data/phen.txt
# varia..."

2017-02-23T17:39:15Z

Created page with "__NO_TITLE__ ==RV-TDT Exercise== vtools init rvtdt vtools import --format vcf data/data.vcf --build hg19 vtools phenotype --from_file data/phen.txt # varia..."

New page

__NO_TITLE__

==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 --recode12 --me 1 1 --set-me-missing --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.*