struct
open Biokepi_run_environment
open Common
module Remove = Workflow_utilities.Remove
| (**
Expects the tool |
let empty_vcf = "##fileformat=VCFv4.1
##source=VarScan2
##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">
##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">
##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">
##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">
##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">
##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">
##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">
##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description=\"Depth of variant-supporting bases (reads2)\">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">
##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR
"
let somatic_on_region
~run_with ?adjust_mapq ~normal ~tumor ~result_prefix region =
let open KEDSL in
let name = Filename.basename result_prefix in
let result_file suffix = result_prefix ^ suffix in
let varscan_tool = Machine.get_tool run_with Machine.Tool.Default.varscan in
let snp_output = result_file "-snp.vcf" in
let indel_output = result_file "-indel.vcf" in
let normal_pileup = Samtools.mpileup ~run_with ~region ?adjust_mapq normal in
let tumor_pileup = Samtools.mpileup ~run_with ~region ?adjust_mapq tumor in
let host = Machine.as_host run_with in
let tags = [Target_tags.variant_caller; "varscan"] in
let varscan_somatic =
let name = "somatic-" ^ name in
let make =
let big_one_liner =
"if [ -s " ^ normal_pileup#product#path
^ " ] && [ -s " ^ tumor_pileup#product#path ^ " ] ; then "
^ sprintf "java -jar $VARSCAN_JAR somatic %s %s --output-snp %s --output-indel %s --output-vcf 1 ; "
normal_pileup#product#path
tumor_pileup#product#path
snp_output
indel_output
^ " else "
^ "echo '" ^ empty_vcf ^ "' > " ^ snp_output ^ " ; "
^ "echo '" ^ empty_vcf ^ "' > " ^ indel_output ^ " ; "
^ " fi "
in
Program.(Machine.Tool.init varscan_tool && sh big_one_liner)
|> Machine.run_big_program run_with ~name ~processors:1
~self_ids:["varscan"; "somatic"]
in
workflow_node ~name ~make
(single_file snp_output ~host)
~tags
~edges:[
depends_on (Machine.Tool.ensure varscan_tool);
depends_on normal_pileup;
depends_on tumor_pileup;
on_failure_activate (Remove.file ~run_with snp_output);
on_failure_activate (Remove.file ~run_with indel_output);
]
in
let snp_filtered = result_file "-snpfiltered.vcf" in
let indel_filtered = result_file "-indelfiltered.vcf" in
let varscan_filter =
let name = "filter-" ^ name in
let make =
Program.(
Machine.Tool.init varscan_tool
&& shf "java -jar $VARSCAN_JAR somaticFilter %s --indel-file %s --output-file %s"
snp_output
indel_output
snp_filtered
&& shf "java -jar $VARSCAN_JAR processSomatic %s" snp_filtered
&& shf "java -jar $VARSCAN_JAR processSomatic %s" indel_output
)
|> Machine.run_big_program run_with ~name ~processors:1
~self_ids:["varscan"; "somaticfilter"]
in
workflow_node ~name ~make ~tags
(vcf_file snp_filtered
~reference_build:normal#product#reference_build ~host)
~edges:[
depends_on varscan_somatic;
on_failure_activate (Remove.file ~run_with snp_filtered);
on_failure_activate (Remove.file ~run_with indel_filtered);
]
in
varscan_filter
let somatic_map_reduce
?(more_edges = []) ~run_with ?adjust_mapq
~normal ~tumor ~result_prefix () =
let run_on_region region =
let result_prefix = result_prefix ^ "-" ^ Region.to_filename region in
somatic_on_region ~run_with
?adjust_mapq ~normal ~tumor ~result_prefix region in
let reference =
Machine.get_reference_genome run_with normal#product#reference_build in
let targets =
List.map (Reference_genome.major_contigs reference)
~f:run_on_region in
let final_vcf = result_prefix ^ "-merged.vcf" in
Vcftools.vcf_concat ~run_with targets ~final_vcf ~more_edges
end