For beagle version 4 some parameters changed

ISUgenomics · May 24, 2016 · b03fed8 · b03fed8
1 parent d8e1bfa
commit b03fed8
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/beagle_PhaseImpute_VCF.sh b/beagle_PhaseImpute_VCF.sh
@@ -10,16 +10,16 @@ OUTPUT=$(basename ${INPUT%.*})
 
 awk '(/#/ || ($4!~"," && $5!~"," && length($4)==1 && length($5)==1))' ${INPUT} > ${OUTPUT}_biAllelic.vcf
 module use /data021/GIF/software/modules
-module load java/1.7.0_76
+#module load java/1.7.0_76
+module load java/1.8.0_25-b17
 module load beagle
 
+java -jar $beagle nthreads=16 window=500000 ibd=true gtgl=psojae_47pop.sort.biallelic.vcf out=psojae_47pop.sort.biallelic_phasedImputed
 
 java -Xmx100g -jar ${beagle} \
  nthreads=16 \
- window=500000 \
- phase-its=40 \
- impute-its=10 \
+ window=50000 \
  ibd=true \
  gtgl=${OUTPUT}_biAllelic.vcf \
- out=${OUTPUT}_PhasedImputed.vcf
+ out=${OUTPUT}_PhasedImputed