Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

Trouble using CombineReadCounts

Sahar90Sahar90 Broad InstituteMember, Broadie
edited February 2017 in Ask the GATK team


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 ?




Sign In or Register to comment.