Mutectcaller with tumor-normal pair returned only haeder vcf

Healthcare & Life Sciences Parabricks
1

Hi there,

I’m testing the somatic pipeline, both tumor only and tumor-normal pair. While the tumor only gave me results, the tumor-normal pair returned me a vcf that contain only the header.
There’s something I could do?
Thanks in advice.

2

Hi Stefano,

can you please provide the command line you are using?

This happens when sample or read group ID is the same for normal and tumor bam

Best
Myrieme

3

Hi Myrieme,

Ok first I used the somatic pipeline command line:

time ./parabricks_install/parabricks/pbrun somatic
–ref /hpcshare/genomics/references/gatk_bundle/reference/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta
–in-tumor-fq /hpcshare/smarangoni/pbrun_file_io/PD_twins/SG_PD-7107_B/PD-7107_S4_R1_001.fastq.gz /hpcshare/smarangoni/pbrun_file_io/PD_twins/SG_PD-7107_B/PD-7107_S4_R2_001.fastq.gz
–knownSites /hpcshare/genomics/references/gatk_bundle/resources/resources_broad_hg38_v0_hapmap_3.3.hg38.vcf.gz
–out-tumor-bam /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107_B.bam
–out-vcf /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107.vcf
–out-tumor-recal-file /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107_B_recal.txt
–in-normal-fq /hpcshare/smarangoni/pbrun_file_io/PD_twins/SG_PD-7107_P/PD-7108_S6_R1_001.fastq.gz /hpcshare/smarangoni/pbrun_file_io/PD_twins/SG_PD-7107_P/PD-7108_S6_R2_001.fastq.gz
–out-normal-bam /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107_P.bam
–out-normal-recal-file /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107_P_recal.txt

Then I also used the mutectcaller tool using this command line:

time ./parabricks_install/parabricks/pbrun mutectcaller
–ref /hpcshare/genomics/references/gatk_bundle/reference/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta
–in-normal-bam /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107_P.bam
–in-normal-recal-file /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107_P_recal.txt
–out-vcf /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107.vcf
–normal-name normal
–tumor-name tumor
–in-tumor-bam /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107_B.bam
–in-tumor-recal-file /hpcshare/smarangoni/pbrun_file_io/PD_twins/PD-7107_B_recal.txt.