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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!