Merge pull request #26 from aryarm/patch/varscan-iupac

handle varscan iupac ambiguity codes

Author: aryarm

callers/varscan

@@ -13,4 +13,5 @@ output_dir="$4"
 
 samtools mpileup -l "$peaks" -f "$genome" -B "$bam" | \
 varscan mpileup2cns --p-value 1 --strand-filter 0 --output-vcf > "$output_dir/varscan.vcf" && \
-bgzip -f "$output_dir/varscan.vcf" && tabix -p vcf -f "$output_dir/varscan.vcf.gz"
+awk -F $"\t" -v 'OFS=\t' '/^#/ || $4 !~ /^(R|Y|M|W|S|K|V|H|D|B|N)$/' "$output_dir/varscan.vcf" | \
+bgzip > "$output_dir/varscan.vcf.gz" && tabix -p vcf -f "$output_dir/varscan.vcf.gz"