fix: umi coverage qc (#1490)

#### Changed - Renamed UMI bamfile in order for the sample id to be unique un multiqc_data.json and not overwritten by hsmetrics.
Clinical-Genomics · Oct 17, 2024 · d3dc977 · d3dc977
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commit d3dc977
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Showing 5 changed files with 10 additions and 9 deletions.
diff --git a/BALSAMIC/snakemake_rules/umi/qc_umi.rule b/BALSAMIC/snakemake_rules/umi/qc_umi.rule
@@ -5,7 +5,7 @@
 
 rule picard_umiaware:
     input:
-        bam = umi_dir + "{sample_type}.{sample}.consensusfiltered_umi.bam"
+        bam = umi_dir + "{sample_type}.{sample}_consensusfiltered_umi.bam"
     output:
         bam = umi_qc_dir + "{sample_type}.{sample}.picard.umiaware.bam",
         duplicates = umi_qc_dir + "{sample_type}.{sample}.umi.duplicatemetrics.txt",
@@ -36,7 +36,7 @@ UMI_METRICS={output.umimetrics};
 
 rule picard_collecthsmetrics_umi:
     input:
-        bam = umi_dir + "{sample_type}.{sample}.consensusfiltered_umi.bam",
+        bam = umi_dir + "{sample_type}.{sample}_consensusfiltered_umi.bam",
         bed = config["panel"]["capture_kit"],
         fa = config["reference"]["reference_genome"],
         fadict = (config["reference"]["reference_genome"]).replace(".fasta",".dict"),
@@ -78,7 +78,7 @@ METRIC_ACCUMULATION_LEVEL=ALL_READS;
 
 rule samtools_view_calculatemeanfamilydepth_umi:
     input:
-        bam = umi_dir + "{sample_type}.{sample}.consensusfiltered_umi.bam"
+        bam = umi_dir + "{sample_type}.{sample}_consensusfiltered_umi.bam"
     output:
         temp_fl = temp (umi_qc_dir + "{sample_type}.{sample}.umi.temp.fl"),
         totalsum = umi_qc_dir + "{sample_type}.{sample}.umi.mean_family_depth"

diff --git a/BALSAMIC/snakemake_rules/umi/sentieon_consensuscall.rule b/BALSAMIC/snakemake_rules/umi/sentieon_consensuscall.rule
@@ -92,7 +92,7 @@ rule sentieon_consensusfilter_umi:
     input:
         umi_dir + "{sample_type}.{sample}.consensuscalled_umi.bam"
     output:
-        umi_dir + "{sample_type}.{sample}.consensusfiltered_umi.bam"
+        umi_dir + "{sample_type}.{sample}_consensusfiltered_umi.bam"
     benchmark:
         Path(benchmark_dir, "sentieon_consensusfilter_umi_{sample_type}_{sample}.tsv").as_posix()
     singularity:
@@ -119,7 +119,7 @@ samtools index {output};
 
 rule bam_compress_tumor_umi:
     input:
-        bam = umi_dir + "tumor.{sample}.consensusfiltered_umi.bam",
+        bam = umi_dir + "tumor.{sample}_consensusfiltered_umi.bam",
         fasta = config_model.reference["reference_genome"]
     output:
         cram = umi_dir + "tumor.{sample}.consensusfiltered_umi.cram",
@@ -143,7 +143,7 @@ samtools index {output.cram};
 if config['analysis']['analysis_type'] == "paired":
     rule bam_compress_normal_umi:
         input:
-            bam = umi_dir + "normal.{sample}.consensusfiltered_umi.bam",
+            bam = umi_dir + "normal.{sample}_consensusfiltered_umi.bam",
             fasta = config_model.reference["reference_genome"]
         output:
             cram = umi_dir + "normal.{sample}.consensusfiltered_umi.cram"

diff --git a/BALSAMIC/snakemake_rules/umi/sentieon_varcall_tnscope.rule b/BALSAMIC/snakemake_rules/umi/sentieon_varcall_tnscope.rule
@@ -7,7 +7,7 @@
 
 rule sentieon_tnscope_umi:
     input:
-        bam = expand(umi_dir + "tumor.{sample}.consensusfiltered_umi.bam", sample=tumor_sample),
+        bam = expand(umi_dir + "tumor.{sample}_consensusfiltered_umi.bam", sample=tumor_sample),
         ref_fa = config["reference"]["reference_genome"],
         bed = config["panel"]["capture_kit"],
         dbsnp = config["reference"]["dbsnp"]

diff --git a/BALSAMIC/snakemake_rules/umi/sentieon_varcall_tnscope_tn.rule b/BALSAMIC/snakemake_rules/umi/sentieon_varcall_tnscope_tn.rule
@@ -6,8 +6,8 @@
 
 rule sentieon_tnscope_umi_tn:
     input:
-        bamT = expand(umi_dir + "tumor.{sample}.consensusfiltered_umi.bam", sample=tumor_sample),
-        bamN = expand(umi_dir + "normal.{sample}.consensusfiltered_umi.bam", sample=normal_sample),
+        bamT = expand(umi_dir + "tumor.{sample}_consensusfiltered_umi.bam", sample=tumor_sample),
+        bamN = expand(umi_dir + "normal.{sample}_consensusfiltered_umi.bam", sample=normal_sample),
         ref_fa = config["reference"]["reference_genome"],
         bed = config["panel"]["capture_kit"],
         dbsnp = config["reference"]["dbsnp"]

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -36,6 +36,7 @@ Changed:
 * Lowered maximal SOR for TNscope in TGA tumor only cases from 3 to 2.7 https://github.com/Clinical-Genomics/BALSAMIC/pull/1475
 * Fixed TNscope research VCF filters to either PASS or triallelic site https://github.com/Clinical-Genomics/BALSAMIC/pull/1475
 * Increased maximal amount of redirects for lychee test following links in docs to 10 https://github.com/Clinical-Genomics/BALSAMIC/pull/1488
+* Renamed UMI consensusfiltered bamfile to be picked up by multiqc https://github.com/Clinical-Genomics/BALSAMIC/pull/1490
 
 Removed:
 ^^^^^^^^