Added parsing mask bed file

drpatelh · Dec 10, 2020 · 98656b4 · 98656b4
1 parent 582aa92
commit 98656b4
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/main.nf b/main.nf
@@ -1389,12 +1389,17 @@ process VARSCAN2_CONSENSUS {
         -bga \\
         -ibam ${bam[0]} \\
         -g $fasta \\
-        | awk '\$4 < $params.min_coverage' | bedtools merge > ${prefix}.mask.bed
+        | awk '\$4 < $params.min_coverage' > ${prefix}.lowcov.bed
+
+    parse_mask_bed.py ${vcf[0]} ${prefix}.lowcov.bed ${prefix}.lowcov.fix.bed
+
+    bedtools merge -i ${prefix}.lowcov.fix.bed > ${prefix}.mask.bed
 
     bedtools maskfasta \\
         -fi $fasta \\
         -bed ${prefix}.mask.bed \\
         -fo ${index_base}.ref.masked.fa
+
     cat ${index_base}.ref.masked.fa | bcftools consensus ${vcf[0]} > ${prefix}.consensus.masked.fa
 
     header=\$(head -n 1 ${prefix}.consensus.masked.fa | sed 's/>//g')