Merge pull request #124 from martinghunt/expose_filter_opts

Expose filter opts

python/clockwork/tasks/variant_call_one_sample.py

@@ -23,4 +23,11 @@ def run(options):
         debug=options.debug,
         keep_bam=options.keep_bam,
         trim_reads=not options.no_trim,
+        minos_filter_min_dp=options.filter_min_dp,
+        minos_filter_min_frs=options.filter_min_frs,
+        minos_filter_min_gcp=options.filter_min_gcp,
+        minos_filter_max_dp=options.filter_max_dp,
+        gvcf_to_fasta_ignore_minos_pass=options.fasta_allow_minos_filter_fail,
+        gvcf_to_fasta_min_frs=options.fasta_min_frs,
+        gvcf_to_fasta_min_dp=options.fasta_min_dp,
     )

python/clockwork/var_call_one_sample_pipeline.py

@@ -28,6 +28,13 @@ def run(
     debug=False,
     keep_bam=False,
     trim_reads=True,
+    minos_filter_min_dp=2,
+    minos_filter_min_frs=0.9,
+    minos_filter_min_gcp=0.5,
+    minos_filter_max_dp=3.0,
+    gvcf_to_fasta_ignore_minos_pass=False,
+    gvcf_to_fasta_min_frs=0.9,
+    gvcf_to_fasta_min_dp=2,
 ):
     if len(reads1_list) != len(reads2_list):
         raise Exception(
@@ -153,7 +160,7 @@ def run(
         minos_vcf_has_vars = False
     else:
         minos_dir = os.path.join(outdir, "minos")
-        cmd = f"minos adjudicate --reads {rmdup_bam} {minos_dir} {refdir.ref_fasta} {samtools_vcf} {cortex_vcf}"
+        cmd = f"minos adjudicate --filter_min_dp {minos_filter_min_dp} --filter_min_frs {minos_filter_min_frs} --filter_min_gcp {minos_filter_min_gcp} --filter_max_dp {minos_filter_max_dp} --reads {rmdup_bam} {minos_dir} {refdir.ref_fasta} {samtools_vcf} {cortex_vcf}"
         utils.syscall(cmd)
         os.rename(os.path.join(minos_dir, "final.vcf"), final_vcf)
         if not debug:
@@ -165,7 +172,7 @@ def run(
     )
     if not debug:
         os.unlink(samtools_gvcf)
-    gvcf.gvcf_to_fasta(final_gvcf, f"{final_gvcf}.fasta")
+    gvcf.gvcf_to_fasta(final_gvcf, f"{final_gvcf}.fasta", require_minos_pass=gvcf_to_fasta_ignore_minos_pass, min_frs=gvcf_to_fasta_min_frs, min_dp=gvcf_to_fasta_min_dp)
 
     if not (keep_bam or debug):
         os.unlink(rmdup_bam)

python/scripts/clockwork

@@ -971,6 +971,53 @@ subparser_variant_call_one_sample.add_argument(
     action="store_true",
     help="Skip read trimming stage at start of pipeline",
 )
+subparser_variant_call_one_sample.add_argument(
+    "--filter_min_dp",
+    type=int,
+    default=2,
+    help="Minimum depth filter cutoff (same as minos option --filter_min_dp) in final VCF file [%(default)s]",
+    metavar="INT",
+)
+subparser_variant_call_one_sample.add_argument(
+    "--filter_min_frs",
+    type=float,
+    default=0.9,
+    help="Minimum FRS filter cutoff (same as minos option --filter_min_frs) in final VCF file [%(default)s]",
+    metavar="FLOAT",
+)
+subparser_variant_call_one_sample.add_argument(
+    "--filter_min_gcp",
+    type=float,
+    default=0.5,
+    help="Minimum GCP filter cutoff (same as minos option --filter_min_gcp) in final VCF file [%(default)s]",
+    metavar="FLOAT",
+)
+subparser_variant_call_one_sample.add_argument(
+    "--filter_max_dp",
+    type=float,
+    default=3.0,
+    help="Determines maximum depth filter cutoff (same as minos option --filter_max_dp) in final VCF file. Using a value of 'x' here sets the cutoff to be more than x standard deviations from the mean read depth [%(default)s]",
+    metavar="FLOAT",
+)
+subparser_variant_call_one_sample.add_argument(
+    "--fasta_allow_minos_filter_fail",
+    action="store_true",
+    help="When making consensus fasta, ignore whether or not PASS is in the FILTER column of minos calls. Default is to put an N whenever there is a filter fail",
+)
+subparser_variant_call_one_sample.add_argument(
+    "--fasta_min_frs",
+    type=float,
+    help="When making consensus fasta, minimum fraction of reads (FRS) required supporting the call. If FRS is less than the given value, then N is added to the FASTA [%(default)s]",
+    default=0.9,
+    metavar="FLOAT",
+)
+subparser_variant_call_one_sample.add_argument(
+    "--fasta_min_dp",
+    type=int,
+    help="When making consensus fasta, minimum total read depth. If depth is less than this, then N is added to the FASTA [%(default)s]",
+    default=2,
+    metavar="INT",
+)
 subparser_variant_call_one_sample.add_argument(
     "ref_dir", help="Directory of reference files, made by clockwork reference_prepare"
 )

scripts/install_dependencies.sh

@@ -260,4 +260,4 @@ pip3 install .
 
 #________________________ minos _____________________________#
 pip3 install 'cluster_vcf_records==0.13.3'
-pip3 install git+https://github.com/iqbal-lab-org/minos@v0.12.5
+pip3 install git+https://github.com/iqbal-lab-org/minos@v0.12.6