Update fingerprinting_dag.py

Update GATK version used

Author: dmcmanam

Fingerprinting/fingerprinting_dag.py

@@ -122,15 +122,15 @@ def fingerprint(project_id):
 
         EXECUTION_DIR = STATS_DIR + 'VCF/'
         output_vcf = EXECUTION_DIR + 'vcf_' + project_id + '/' + patient_id + '__' + project_id + '__' + igoId + '.vcf'
-        command1 = 'bsub -J "extract_fingerprint_{}" /home/igo/resources/gatk-4.1.9.0/gatk ExtractFingerprint --VALIDATION_STRINGENCY \'SILENT\' --HAPLOTYPE_MAP \'{}\'  --INPUT \'{}\' --OUTPUT \'{}\' --REFERENCE_SEQUENCE \'{}\' --SAMPLE_ALIAS \'{}\''.format(igoId, HAPLOTYPE_MAP, bam, output_vcf, REFERENCE_SEQUENCE, patient_id)
+        command1 = 'bsub -J "extract_fingerprint_{}" /home/igo/resources/gatk-4.6.1.0/gatk ExtractFingerprint --VALIDATION_STRINGENCY \'SILENT\' --HAPLOTYPE_MAP \'{}\'  --INPUT \'{}\' --OUTPUT \'{}\' --REFERENCE_SEQUENCE \'{}\' --SAMPLE_ALIAS \'{}\''.format(igoId, HAPLOTYPE_MAP, bam, output_vcf, REFERENCE_SEQUENCE, patient_id)
         subprocess.call(command1, shell=True)
         print("Running extract fingerprint: " + command1)
         vcfs.append(output_vcf)
 
     extractFingerprint_finish = process_time()
     print('Elapsed time to extract fingerprint for all bams: ', extractFingerprint_finish - extractFingerprint_start)
     # TODO redirect bsub output to file and check return value of the command?
-    command_crosscheck = 'bsub -K -n 9 -M 6 -w "ended(extract_fingerprint_*)" -J "CrosscheckFingerprint_{}" /home/igo/resources/gatk-4.1.9.0/gatk CrosscheckFingerprints LOD_THRESHOLD=-5.0 CROSSCHECK_BY=FILE NUM_THREADS=30 OUTPUT=/igo/staging/stats/VCF/vcf_{}/crosscheck_fingerprint_{}.tsv HAPLOTYPE_MAP=\'{}\' INPUT='.format(project_id, project_id, project_id, HAPLOTYPE_MAP)    
+    command_crosscheck = 'bsub -K -n 9 -M 6 -w "ended(extract_fingerprint_*)" -J "CrosscheckFingerprint_{}" /home/igo/resources/gatk-4.6.1.0/gatk CrosscheckFingerprints LOD_THRESHOLD=-5.0 CROSSCHECK_BY=FILE NUM_THREADS=30 OUTPUT=/igo/staging/stats/VCF/vcf_{}/crosscheck_fingerprint_{}.tsv HAPLOTYPE_MAP=\'{}\' INPUT='.format(project_id, project_id, project_id, HAPLOTYPE_MAP)    
     vcfInputs = " INPUT=".join(vcfs)
 
     command_crosscheck += vcfInputs
@@ -284,4 +284,4 @@ def get_igo_id_mappings(sample_manifests, mapped_fields):
         exit(1)
 
     project_id = sys.argv[1]
-    fingerprint(project_id)
+    fingerprint(project_id)