Attention: Want an end-to-end pipelining solution for GATK Best Practices?
Trouble using CombineReadCounts
I am trying to create a PoN following
I ran "GATK 4 CNV Proportional Coverage for Capture" and compiled the paths of the normal samples in one file (attached: listPropCov_TSCA11_15.txt)
I tried to run CombineReadCounts as follows using GATK4alpha (I tried using GATK3.7 but it gave a different error):
pathToGATK_jar = "....../gatk4-latest/gatk-protected.jar"
pathTotext_file_list_of_proportional_coverage_files = "....../listPropCov_TSCA11_15.txt"
pathToOutputFile = "...../merged_prop_cov_TSCA11_15.tsv"
javaPath = "/broad/software/free/Linux/redhat_6_x86_64/pkgs/jdk1.8.0_121/bin/java"
command = paste0(javaPath," -Xmx8g -jar ",pathToGATK_jar," CombineReadCounts --inputList ", pathTotext_file_list_of_proportional_coverage_files," -O ",pathToOutputFile, " -MOF 0")
And I got the following error:
"A USER ERROR has occurred: Bad input: the input contains the sample repeated, e.g.:A3"
I checked my sample names and all of them are unique, I also checked that the interval names are unique. I tried using only 46 samples, but it gave me the same error.
What am I doing wrong? Is there another way to create a panel of normals to be used in GATK_Somatic_CNV_Toolchain_Capture ?