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[BENCHMARK] dataset comparison: new datasets #244

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a8f17a7
[TEST] Download new Datasets
Irallia Oct 5, 2022
5d23d8b
[TEST] Update iGenVar only workflow
Irallia Oct 5, 2022
38cce5e
tmp leave out S4
Irallia Nov 21, 2022
db3470a
[DOC] Update plots
Irallia Nov 21, 2022
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71 changes: 55 additions & 16 deletions test/benchmark/caller_comparison_iGenVar_only/workflow/rules/callers.smk
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
sample = config["parameters"]["sample"],
sample_HG002 = config["parameters"]["sample_HG002"],
sample_NA12878 = config["parameters"]["sample_NA12878"],
min_var_length = config["parameters"]["min_var_length"],
max_var_length = config["parameters"]["max_var_length"]

Expand All @@ -13,111 +14,149 @@ rule run_iGenVar:
short_bam = config["short_read_bam"]["s1"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S2': # Illumina Mate Pair
short_bam = config["short_read_bam"]["s2"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S3': # Illumina HiSeq
short_bam = config["short_read_bam"]["s3"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S4': # NA12878 WGS GRCh38
short_bam = config["short_read_bam"]["s4"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
--output {output.vcf} --vcf_sample_name {sample_NA12878} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S1L1': # Illumina Paired End & MtSinai PacBio
short_bam = config["short_read_bam"]["s1"],
long_bam = config["long_read_bam"]["l1"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S2L1': # Illumina Mate Pair & MtSinai PacBio
short_bam = config["short_read_bam"]["s2"],
long_bam = config["long_read_bam"]["l1"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S3L1': # Illumina HiSeq & MtSinai PacBio
short_bam = config["short_read_bam"]["s3"],
long_bam = config["long_read_bam"]["l1"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S1L2': # Illumina Paired End & PacBio CCS
short_bam = config["short_read_bam"]["s1"],
long_bam = config["long_read_bam"]["l2"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S2L2': # Illumina Mate Pair & PacBio CCS
short_bam = config["short_read_bam"]["s2"],
long_bam = config["long_read_bam"]["l2"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S3L2': # Illumina HiSeq & PacBio CCS
short_bam = config["short_read_bam"]["s3"],
long_bam = config["long_read_bam"]["l2"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S1L3': # Illumina Paired End & 10X Genomics
short_bam = config["short_read_bam"]["s1"],
long_bam = config["long_read_bam"]["l3"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S2L3': # Illumina Mate Pair & 10X Genomics
short_bam = config["short_read_bam"]["s2"],
long_bam = config["long_read_bam"]["l3"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'S3L3': # Illumina HiSeq & 10X Genomics
short_bam = config["short_read_bam"]["s3"],
long_bam = config["long_read_bam"]["l3"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'L1': # MtSinai PacBio
long_bam = config["long_read_bam"]["l1"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'L2': # PacBio CCS
long_bam = config["long_read_bam"]["l2"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'L3': # 10X Genomics
long_bam = config["long_read_bam"]["l3"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_long_reads {long_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'hg38_Sim_default': # Illumina
short_bam = config["simulated_short_read_bam"]["sim1"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'hg38_Sim_InDel': # Illumina
short_bam = config["simulated_short_read_bam"]["sim2"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
elif wildcards.input_combination == 'hg38_Sim_noSNP': # Illumina
short_bam = config["simulated_short_read_bam"]["sim3"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
else: # wildcards.input_combination == 'hg38_Sim_SNPandSV': # Illumina
short_bam = config["simulated_short_read_bam"]["sim4"]
shell("""
/usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
--output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
--output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
--min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
""")
# Defaults:
Expand Down
18 changes: 15 additions & 3 deletions test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.DEL.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,8 @@ rule truvari_DEL:
"logs/truvari/truvari_output.{input_combination}.{min_qual}.log"
params:
output_dir = "results/caller_comparison_iGenVar_only/eval/{input_combination}/DEL.min_qual_{min_qual}",
truth_set_gz = config["truth_set_DEL_renamed_chr"]["gz"],
truth_set_bed = config["truth_set_renamed_chr"]["bed"]
truth_set_gz = config["truth_set_HG002_DEL_renamed_chr"]["gz"],
truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
shell:
"""
rm -rf {params.output_dir} && truvari bench -b {params.truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
Expand All @@ -58,6 +58,10 @@ rule cat_truvari_results_DEL:
min_qual = min_qual_iGenVar),
S2 = expand("results/caller_comparison_iGenVar_only/eval/S2/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S3 = expand("results/caller_comparison_iGenVar_only/eval/S3/min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
# S4 = expand("results/caller_comparison_iGenVar_only/eval/S4/min_qual_{min_qual}/pr_rec.txt",
# min_qual = min_qual_iGenVar),
L1 = expand("results/caller_comparison_iGenVar_only/eval/L1/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
L2 = expand("results/caller_comparison_iGenVar_only/eval/L2/DEL.min_qual_{min_qual}/pr_rec.txt",
Expand All @@ -67,6 +71,8 @@ rule cat_truvari_results_DEL:
output:
S1 = temp("results/caller_comparison_iGenVar_only/eval/S1.DEL_results.txt"),
S2 = temp("results/caller_comparison_iGenVar_only/eval/S2.DEL_results.txt"),
S3 = temp("results/caller_comparison_iGenVar_only/eval/S3.all_results.txt"),
# S4 = temp("results/caller_comparison_iGenVar_only/eval/S4.all_results.txt"),
L1 = temp("results/caller_comparison_iGenVar_only/eval/L1.DEL_results.txt"),
L2 = temp("results/caller_comparison_iGenVar_only/eval/L2.DEL_results.txt"),
L3 = temp("results/caller_comparison_iGenVar_only/eval/L3.DEL_results.txt"),
Expand All @@ -75,10 +81,16 @@ rule cat_truvari_results_DEL:
run:
shell("cat {input.S1} > {output.S1}")
shell("cat {input.S2} > {output.S2}")
shell("cat {input.S3} > {output.S3}")
# shell("cat {input.S4} > {output.S4}")
shell("cat {input.L1} > {output.L1}")
shell("cat {input.L2} > {output.L2}")
shell("cat {input.L3} > {output.L3}")
shell("""
cat {output.S1} {output.S2} \
cat {output.S1} {output.S2} {output.S3} \
{output.L1} {output.L2} {output.L3} > {output.all}
""")
# shell("""
# cat {output.S1} {output.S2} {output.S3} {output.S4} \
# {output.L1} {output.L2} {output.L3} > {output.all}
# """)
18 changes: 15 additions & 3 deletions test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.INS.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,8 @@ rule truvari_INS:
"logs/truvari/truvari_output.{input_combination}.{min_qual}.log"
params:
output_dir = "results/caller_comparison_iGenVar_only/eval/{input_combination}/INS.min_qual_{min_qual}",
truth_set_gz = config["truth_set_INS_renamed_chr"]["gz"],
truth_set_bed = config["truth_set_renamed_chr"]["bed"]
truth_set_gz = config["truth_set_HG002_INS_renamed_chr"]["gz"],
truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
shell:
"""
rm -rf {params.output_dir} && truvari bench -b {params.truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
Expand All @@ -58,6 +58,10 @@ rule cat_truvari_results_INS:
min_qual = min_qual_iGenVar),
S2 = expand("results/caller_comparison_iGenVar_only/eval/S2/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S3 = expand("results/caller_comparison_iGenVar_only/eval/S3/min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
# S4 = expand("results/caller_comparison_iGenVar_only/eval/S4/min_qual_{min_qual}/pr_rec.txt",
# min_qual = min_qual_iGenVar),
L1 = expand("results/caller_comparison_iGenVar_only/eval/L1/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
L2 = expand("results/caller_comparison_iGenVar_only/eval/L2/INS.min_qual_{min_qual}/pr_rec.txt",
Expand All @@ -67,6 +71,8 @@ rule cat_truvari_results_INS:
output:
S1 = temp("results/caller_comparison_iGenVar_only/eval/S1.INS_results.txt"),
S2 = temp("results/caller_comparison_iGenVar_only/eval/S2.INS_results.txt"),
S3 = temp("results/caller_comparison_iGenVar_only/eval/S3.all_results.txt"),
# S4 = temp("results/caller_comparison_iGenVar_only/eval/S4.all_results.txt"),
L1 = temp("results/caller_comparison_iGenVar_only/eval/L1.INS_results.txt"),
L2 = temp("results/caller_comparison_iGenVar_only/eval/L2.INS_results.txt"),
L3 = temp("results/caller_comparison_iGenVar_only/eval/L3.INS_results.txt"),
Expand All @@ -75,10 +81,16 @@ rule cat_truvari_results_INS:
run:
shell("cat {input.S1} > {output.S1}")
shell("cat {input.S2} > {output.S2}")
shell("cat {input.S3} > {output.S3}")
# shell("cat {input.S4} > {output.S4}")
shell("cat {input.L1} > {output.L1}")
shell("cat {input.L2} > {output.L2}")
shell("cat {input.L3} > {output.L3}")
shell("""
cat {output.S1} {output.S2} \
cat {output.S1} {output.S2} {output.S3} \
{output.L1} {output.L2} {output.L3} > {output.all}
""")
# shell("""
# cat {output.S1} {output.S2} {output.S3} {output.S4} \
# {output.L1} {output.L2} {output.L3} > {output.all}
# """)
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