Tag: CalculateContamination

gatk – A bash script for running on a bunch of bam files

I have some bam files in this directory /data/Continuum/WES/results/ I want to run GATK mutation calling over bam files I googled and I realised for one function, I can do this cd /data/Continuum/WES/vcf/ for file in *.bam ; do ./gatk CollectSequencingArtifactMetrics -I /data/Continuum/WES/results/NG-27280_CLTSS_LTS_0017_lib506243_7661_2_MarkedDup.bam -O NG-27280_CLTSS_LTS_0017_lib506243_7661_2_MarkedDup –FILE_EXTENSION .txt -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta done;…

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GATK CalculateContamination – zeros in output

GATK CalculateContamination – zeros in output 2 Hi, I am new to exome-seq and would be grateful for any suggestions 🙂 I want to run GATK CalculateContamination (GATK 4.1.8.1), before calling variants with MuTect2. CalculateContamination tool returns “SUCCESS” message, but with warnings, and I get only “0” values in my…

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