Error When Using Depthofcoverage With An Interval File With Gatk

Question

[datanerd]

Hi All,

I am having trouble using DepthOfCoverage over a provided interval file. Although it runs fine if I omit the -L file.

The error that I get is:

A USER ERROR has occurred (version 1.3-20-g447e9bf):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: File associated with name /Users/Desktop//myinterval.bed is malformed: Interval file could not be parsed in any supported format. caused by BED files must be parsed through Tribble; parsing them as intervals through the GATK engine is no longer supported

The format of the file is: chr1:XXXX-XXXXXX also tried 1:XXXXX-XXXXXX

Does anyone know what the problem might be? Is it the interval format? Thanks!

[datanerd]

Btw,

For anyone who has this issue. IT HAS TO DO WITH THE VERSION OF GATK USED. thanks everyone.

[Alex Paciorkowski]

Are you sure you are using the correct interval file for the target your experiment sequenced? Likely if you omit the file, you will not get an accurate depth of coverage across your actual sequenced target. What output do you get with the target file omitted -- and does it make sense? Also, what command are you running that gives you the above error?

[datanerd]

Thanks Alex! Its an exome run.I looked it up for the interval file, and I think it should be fine (an R package https://secure.genome.ucla.edu/index.php/ExomeCNV_User_Guide gives an example for the interval file) although GATK doesnot provide any example file. With -L omitted whatever runs, I think it makes sense (dint let it run completely-shows 40hours to run, so terminated it)

my command: java -jar /path/GenomeAnalysisTK.jar -T DepthOfCoverage -R /path/hg19/ucsc.hg19.fasta -I /path/x.bam -L /pathallexons2.bed -o test.coverage

Answer 1

[Jorge Amigo]

I don't know if the very well known chr1:XXXX-XXXXXX format has previously worked, but the intervals file that GATK needs must be a bed file, hence the following 3-column tabulated format is required:

chr start end

keep in mind that the DepthOfCoverage is a module that has been announced to be retired in the next GATK 2.4 version, which should be coming in a very near future. the GATK team is already suggesting us users to keep an eye on its substitute DiagnoseTargets.

[Ashutosh Pandey]

This should solve it.

Answer 2

[datanerd]

Hi all, The problem was with the version of GATK being too old. Thanks for the replies:)

Answer 3

[samsara]

The problem is in your arguments. You did not provide correct arguments. -T takes name of GATK tool. For example VariantRecalibrator. I think DepthOfCoverage that you have used is not GATK tool.

Answer 4

[vishnusimha13]

Hello guys,

I really have problem in using GATK for indel realignment,

what is this interval file and how exactly we should generate it. Absolutely no idea.

At present, i have my sorted,redup.bam files ready with me.

Kindly help me in using GATK for indelrealigner, BQSR and variant calling,

Thanking you all in tons, Vishnu.

Answer 5

[ivivek_ngs]

I am entirely new with the exome sequencing data analysis. I want to use it for my analysis with paired end reads. I want to play with an established pipeline first and then use it on my data. Can anyone help me with a script pipeline. Moreover , I am having trouble to understand the script format at places where GATK is used. Below is the link of the question I posted. It would be nice if anyone can help me out.

C: Can anyone suggest me a script based pipeline for exome sequencing with paired end reads generated by Illumina for tumor samples.

[samsara]

You can have a look on my pipeline for reference https://www.dropbox.com/s/0nhnm47zn32qzhh/SNPcall.sh used for paired end data.