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author | Justin Bedo <cu@cua0.org> | 2018-10-26 08:05:28 +1100 |
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committer | Justin Bedo <cu@cua0.org> | 2018-10-26 08:05:28 +1100 |
commit | 2c706aaad54aeec0f224ab7c313ac22aebe0bb9e (patch) | |
tree | e6f8e84d12bcc656f2ca50f0c118102bee32d54b /tools/mutect-call.nix | |
parent | 4ee3f9f9c24b7dcdaa1be19aadd84454219c43f6 (diff) |
init: mutect
Diffstat (limited to 'tools/mutect-call.nix')
-rw-r--r-- | tools/mutect-call.nix | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/tools/mutect-call.nix b/tools/mutect-call.nix new file mode 100644 index 0000000..9fd009b --- /dev/null +++ b/tools/mutect-call.nix @@ -0,0 +1,42 @@ +{bionix +, nixpkgs +, cosmic +, dbsnp}: + +with nixpkgs; +with lib; + +let + inherit (bionix.types) matchFiletype; + getVCFref = matchFiletype "mutect-call" {vcf = {ref}: ref;}; + getBAMref = matchFiletype "mutect-call" {bam = {ref, ...}: ref;}; + refs = map getVCFref [ cosmic dbsnp ]; + ref = head refs; +in + +assert (length (unique refs) == 1); + +{normal, tumour}: + +assert (ref == getBAMref normal && ref == getBAMref tumour); + +stdenv.mkDerivation { + name = "mutect"; + buildInputs = [ bionix.mutect.app ]; + buildCommand = '' + ln -s ${normal} normal.bam + ln -s ${tumour} tumour.bam + ln -s ${dbsnp} dbsnp.vcf + ln -s ${cosmic} cosmic.vcf + ln -s ${ref} ref.fa + ln -s ${bionix.samtools.faidx {} ref} ref.fa.fai + ln -s ${bionix.samtools.dict {} ref} ref.dict + mutect --analysis_type MuTect \ + --reference_sequence ref.fa \ + --cosmic cosmic.vcf \ + --dbsnp dbsnp.vcf \ + --input_file:normal normal.bam \ + --input_file:tumour tumour.bam \ + --out $out + ''; +} |