-
Notifications
You must be signed in to change notification settings - Fork 0
/
assoc.sh
18 lines (17 loc) · 1 KB
/
assoc.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
awk -vdis=$dis '($1==dis){print $2}' ../data/maf01_mac3.dat > ../results/dis/${dis}.markers
awk -vdis=$dis 'NR==FNR{m[$1]=1;next} ($1 in m){gs[$3]=gs[$3]"\t"$2} END{for(g in gs)print g gs[g]}' ../results/dis/${dis}.markers ../data/genes.anno > ../results/dis/${dis}.genes
Rscript step2_SPAtests.R \
--vcfFile=../data/allchr_revel.vcf.gz \
--vcfFileIndex=../data/allchr_revel.vcf.gz.tbi \
--vcfField=DS \
--IsDropMissingDosages=FALSE \
--minMAF=0 \
--minMAC=0.5 \
--GMMATmodelFile=../data/dis/${dis}/${dis}.rda \
--varianceRatioFile=../data/dis/${dis}/${dis}.varianceRatio.txt \
--SAIGEOutputFile=../results/dis/${dis}.SAIGE.gene.txt \
--LOCO=FALSE \
--groupFile=../results/dis/${dis}.genes \
--sparseSigmaFile=../data/dis/${dis}/${dis}.varianceRatio.txt_relatednessCutoff_0.125_2000_randomMarkersUsed.sparseSigma.mtx \
--dosageZerodCutoff=0 \
--IsSingleVarinGroupTest=TRUE > ../results/dis/${dis}.log