allows for larger read depth (5000)

mfiers · Jun 19, 2012 · 881758f · 881758f
1 parent 66d46c4
commit 881758f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/template2/recursive_map.jinja2 b/template2/recursive_map.jinja2
@@ -38,7 +38,7 @@ lasti=0
     echo "bamfiles collected: ${bamfiles}"
     if [[ ! -f variants.{{i}}.vcf ]]
     then
-        samtools mpileup -uf $reference \
+        samtools mpileup -C50 -d 5000 -L 5000 -uf $reference \
             ${bamfiles} \
             | bcftools view -bvcg - \
             > variants.raw.{{i}}.bcf