merge BAM files for replicates

dunnart/Snakefile

@@ -189,6 +189,20 @@ rule indexBam:
     shell:
         "samtools index -c {input} {output} 2> {log}"
 
+rule mergeBAMreplicates:
+    input:
+        H3K4me3 = ["results/bowtie2/A-2_H3K4me3_PPq30.sorted.dedup.bam,  results/bowtie2/B-2_H3K4me3_PPq30.sorted.dedup.bam"],
+        H3K27ac = ["results/bowtie2/A-3_H3K27ac_PPq30.sorted.dedup.bam, results/bowtie2/B-3_H3K27ac_PPq30.sorted.dedup.bam"]
+    output:
+        H3K4me3 = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
+        H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam"
+    log:
+        H3K4me3 = "logs/H3K4me3.mergeBAM",
+        H3K27ac = "logs/H3K27ac.mergeBAM"
+    run:
+        shell("samtools merge {output.H3K4me3} {input.H3K4me3} 2> {log.H3K4me3}")
+        shell("samtools merge {output.H3K27ac} {input.H3K427ac} 2> {log.H3K27ac}")
+
 # ===============================================================================================
 #  4. GENERAL ALIGNMENT QC
 #   > SAMtools flagstat statistics