jujojujo Posts: 3Member


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 and used the script 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!



  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,369Administrator, GATK Developer admin

    Hi there,

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

    Geraldine Van der Auwera, PhD

  • jujojujo Posts: 3Member
    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:

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

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

    Post edited by jujo on
  • pdexheimerpdexheimer Posts: 439Member, GSA Collaborator ✭✭✭✭

    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

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