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Trouble using CombineReadCounts

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

Hi,

I am trying to create a PoN following
http://gatkforums.broadinstitute.org/gatk/discussion/6791/description-and-examples-of-the-steps-in-the-cnv-case-and-cnv-pon-creation-workflows#create-pon-workflow

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")

system(command)

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 ?

Thanks!

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