less stringent spike in filter bams

alsmith151 · May 24, 2024 · 2659eed · 2659eed
1 parent ee52c85
commit 2659eed
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/seqnado/workflow/rules/exogenous_norm.smk b/seqnado/workflow/rules/exogenous_norm.smk
@@ -44,7 +44,7 @@ rule filter_bam_spikein:
         "seqnado_output/logs/aligned_spikein/{sample}_filter.log",
     shell:
         """
-    samtools view -b -F 3332 -q 30 -@ 8 {input.bam} > {output.bam} &&
+    samtools view -b -F 256 -f 2 -q 30 -@ 8 {input.bam} > {output.bam} &&
     echo 'Filtered bam number of mapped reads:' > {log} 2>&1 &&
     samtools view -c {output.bam} >> {log} 2>&1
     """