The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

DepthofCoverage

Hi,

im trying to calculate the coverage of a exome sequencing project.

My Code is
java -jar $gatk_jar \ -T DepthOfCoverage \ -R $ref_genome \ -I "$sample_name".recal_reads.bam \ -o $result_dir/$sample_name/coverage/"$sample_name" \ -geneList $ref_refseq \ -L test.bed \ -ct 10 -ct 20 -ct 30
but i get an ERROR that i cant solve...

ERROR MESSAGE: Unknown file is malformed:

Could not parse location from line: chr1 66999814 67000061 NM_032291_exon_0_10_chr1_66999825_f 0 +

This error relates to my refseq_file but i cant find the problem with it. This is the first line from my geneList so something is messed up.

I created it along http://www.broadinstitute.org/gatk/guide/article?id=1329 and used the script sortByRef.pl to sort it by the fai file from your bundle

Can you give me any advise to check on ?

Thank you very much for helping!

Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    Try passing the refseq as -geneList:REFSEQ $ref_refseq to ensure that the file gets parsed using the correct format presets.

  • jujojujo Member
    edited November 2013

    Yeah this solves the error!

    But now I have a new one, which comes from the order of the file. I have tried to use our suggested perl script. My Command:
    `
    MESSAGE: Input file is not sorted by start position.

    ERROR We saw a record with a start of chr1:48998527 after a record with a start of chr1:66999825, for input source: geneTrack.refSeq.sorted.txt

    `
    I know that message is clear but i dont know what is going wrong.

    I called your perl script with:

    ./sortbyref.pl geneTrack.refSeq ucsc.hg19.fasta.fai > geneTrack.refSeq.sorted.txt

    But i guess there is something wrong with that .fai file ?

  • It's been a while since I've used it, but I think that script has a default value (overridden on the command line) for which column contains the actual position values. I think that default must be wrong for your file

Sign In or Register to comment.