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# DepthofCoverage

Member Posts: 3

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 $ref_refseq \ -L test.bed \ -ct 10 -ct 20 -ct 30 but i get an ERROR that i cant solve... ##### ERROR MESSAGE: Unknown file is malformed: Could not parse location from line: chr1 66999814 67000061 NM_032291_exon_0_10_chr1_66999825_f 0 + This error relates to my refseq_file but i cant find the problem with it. This is the first line from my geneList so something is messed up. I created it along http://www.broadinstitute.org/gatk/guide/article?id=1329 and used the script sortByRef.pl to sort it by the fai file from your bundle Can you give me any advise to check on ? Thank you very much for helping! ## Answers • Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin Hi there, Try passing the refseq as -geneList:REFSEQ$ref_refseq to ensure that the file gets parsed using the correct format presets.

Geraldine Van der Auwera, PhD

• Member Posts: 3
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 &gt; geneTrack.refSeq.sorted.txt`

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

• Member, Dev Posts: 544 ✭✭✭✭

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