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DepthOfCoverage: ERROR MESSAGE: Error parsing line at byte position
I am using depthofCoverage tool as shown below:
java -Xmx2g -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R ucsc_hg19.fa -geneList:REFSEQ refGene.bed -L exons.bed -ct 1 -ct 5 -ct 10 -ct 20 -ct 50 -I WT_recalibrated.bam -o cov
Original exons.bed file looks like:
chr1 6526151 6527632 PLEKHG5_1 0 + chr1 6527884 6528646 PLEKHG5_2 0 + chr1 6529101 6529301 PLEKHG5_3 0 + chr1 6529394 6529510 PLEKHG5_4 0 + chr1 6529603 6529736 PLEKHG5_5 0 + chr1 6530295 6530415 PLEKHG5_6 0 + chr1 6530565 6530703 PLEKHG5_7 0 + chr1 6530794 6530944 PLEKHG5_8 0 + chr1 6531049 6531697 PLEKHG5_9 0 +
Then, refGene.bed file is prepared based on the awk solution provided at the thread 'http://gatkforums.broadinstitute.org/discussion/3229/exon-output-depth-of-coverage'
1 PLEKHG5_exon_1 chr1 + 6526151 6527632 6526151 6527632 1 6526151 6527632 0 PLEKHG5 exon_1 cmpl cmpl 0 2 PLEKHG5_exon_2 chr1 + 6527884 6528646 6527884 6528646 1 6527884 6528646 0 PLEKHG5 exon_2 cmpl cmpl 0 3 PLEKHG5_exon_3 chr1 + 6529101 6529301 6529101 6529301 1 6529101 6529301 0 PLEKHG5 exon_3 cmpl cmpl 0 4 PLEKHG5_exon_4 chr1 + 6529394 6529510 6529394 6529510 1 6529394 6529510 0 PLEKHG5 exon_4 cmpl cmpl 0 5 PLEKHG5_exon_5 chr1 + 6529603 6529736 6529603 6529736 1 6529603 6529736 0 PLEKHG5 exon_5 cmpl cmpl 0
However, the above command returns the error:
##### ERROR MESSAGE: Error parsing line at byte position: [email protected], for input source:refGene.bed
Could someone help to fix this. This is not basically a refGene file. This is prepared from a custom exon.bed file which doesn't have refGene notations using the awk solution in the above thread.