added defaults to genotypes

arundurvasula · Jun 9, 2015 · f1a7207 · f1a7207
1 parent b7d0a3c
commit f1a7207
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Showing 2 changed files with 26 additions and 18 deletions.
diff --git a/scripts/ANGSD_genotypes.sh b/scripts/ANGSD_genotypes.sh
@@ -7,6 +7,19 @@ source scripts/common.conf
 # load utils functions
 source ${SCRIPTS_DIR}/utils.sh
 
+DO_MAJORMINOR=1
+UNIQUE_ONLY=0
+MIN_MAPQ=30
+MIN_BASEQUAL=20
+GT_LIKELIHOOD=2
+DO_GENO=7
+DO_POST=1
+POST_CUTOFF=0.95
+DO_MAF=2
+SNP_PVAL=1e-6
+MIN_IND=1
+N_CORES=32
+
 load_config $1
 
 N_IND=`wc -l < ${TAXON_LIST}`
@@ -15,20 +28,17 @@ N_IND=`wc -l < ${TAXON_LIST}`
 ${ANGSD_DIR}/angsd\
   -bam ${TAXON_LIST}\
   -out ./results/${TAXON}_snps\
-  -doMajorMinor 1\
-  -uniqueOnly 0\
-  -minMapQ 30\
-  -minQ 20\
-  -GL 2\
-  -r 12:\
-  -doGeno 7\
-  -doPost 1\
-  -postCutoff 0.95\
-  -doMaf 2\
-  -SNP_pval 1e-6\
+  -doMajorMinor ${DO_MAJORMINOR}\
+  -uniqueOnly ${UNIQUE_ONLY}\
+  -minMapQ ${MIN_MAPQ}\
+  -minQ ${MIN_BASEQUAL}\
+  -GL ${GT_LIKELIHOOD}\
+  -r ${REGIONS}\
+  -doGeno ${DO_GENO}\
+  -doPost ${DO_POST}\
+  -postCutoff ${POST_CUTOFF}\
+  -doMaf ${DO_MAF}\
+  -SNP_pval ${SNP_PVAL}\
   -nInd ${N_IND}\
-  -minInd 4\
-  -P 16
-#  -ref ${REF_SEQ}\
-#  -anc ${ANC_SEQ}
-#  -baq 1
+  -minInd ${MIN_IND}\
+  -P ${N_CORES}
diff --git a/scripts/genotype_example.conf b/scripts/genotype_example.conf
@@ -1,5 +1,3 @@
 TAXON=all
 TAXON_LIST=${DATA_DIR}/${TAXON}_samples.txt
 TAXON_INBREEDING=${DATA_DIR}/${TAXON}_F.txt
-ANC_SEQ=/home/tvkent/projects/rice/data/meridionalis_anc.fa.gz
-REF_SEQ=/home/tvkent/projects/rice/data/riceRefs/Oryza_sativa.IRGSP-1.0.23.dna.genome_chr.fa.gz