ERROR MESSAGE: Unknown file is malformed in DepthOfCoverage
I am using DepthOfCoverage to get the exome coverage of a target reference and getting this error.
ERROR MESSAGE: Unknown file is malformed: Could not parse location from line: chr1 11873 12227 NR_046018_exon_0_0_chr1_11874_f 0 +
My command line is
ava -Xmx64g -jar GenomeAnalysisTK.jar
-I bamfiles.list //A list of paths to bam files
-ct 10 -ct 20 -ct 40 -ct 80 -ct 100
I used AWK to modify the refseq file as from the instructions at https://www.broadinstitute.org/gatk/guide/article?id=1329 and this same command was working when I did to get gene coverage.
So, what am I doing wrong now?