BED file is malformed with unreadable codes

[bjfan]

Although I edited the BED file to remove the headlines and random contigs which is not present in the reference dictionary, I still got the following errors. It seems that there is a contig with unreadable codes (1) in the edited BED file. I could not find a way to remove this kind of contigs from BED file. Could anyone give some advices? Thank you in advance.

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# LSBATCH: User input
# Depth of coverage within targets_interval

java -Xmx32g -jar /home/bf13/GATK/GenomeAnalysisTK-1.6-5-g557da77/GenomeAnalysisTK.jar \
-l INFO \
-T DepthOfCoverage \
-R /home/bf13/RefSeq/human_g1k_v37.fasta \
-L /home/bf13/RefSeq/SureSelect_All_Exon_V4_plus_UTRs_71mb.hg19.rm.bed \
-I jw1028.bam \
-I jw1107.bam \
-I jw1108.bam \
-I jw1661.bam \
-I jw1662.bam \
-I jw1664.bam \
-I jw1780.bam \
-I jw3011.bam \
-I jw3116.bam \
-I jw3139.bam \
-omitBaseOutput \
-o jw_all.depth.coverage \
--outputFormat csv

------------------------------------------------------------

Exited with exit code 1.

Resource usage summary:

CPU time : 8.44 sec.
Max Memory : 2 MB
Max Swap : 35 MB

Max Processes : 1
Max Threads : 1

The output (if any) follows:

INFO 14:32:39,466 RodBindingArgumentTypeDescriptor - Dynamically determined type of /home/bf13/RefSeq/SureSelect_All_Exon_V4_plus_UTRs_71mb.hg19.rm.bed to be BED INFO 14:32:39,513 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:32:39,513 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-5-g557da77, Compiled 2012/05/03 17:30:26 INFO 14:32:39,513 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 14:32:39,514 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:32:39,514 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 14:32:39,515 HelpFormatter - Program Args: -l INFO -T DepthOfCoverage -R /home/bf13/RefSeq/human_g1k_v37.fasta -L /home/bf13/RefSeq/SureSelect_All_Exon_V4_plus_UTRs_71mb.hg19.rm.bed -I jw1028.bam -I jw1107.bam -I jw1108.bam -I jw1661.bam -I jw1662.bam -I jw1664.bam -I jw1780.bam -I jw3011.bam -I jw3116.bam -I jw3139.bam -omitBaseOutput -o jw_all.depth.coverage --outputFormat csv INFO 14:32:39,515 HelpFormatter - Date/Time: 2012/06/06 14:32:39 INFO 14:32:39,515 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:32:39,515 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:32:39,540 GenomeAnalysisEngine - Strictness is SILENT INFO 14:32:39,624 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 14:32:40,693 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 1.07 INFO 14:32:42,984 GATKRunReport - Uploaded run statistics report to AWS S3 ##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.6-5-g557da77):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: File associated with name /home/bf13/RefSeq/SureSelect_All_Exon_V4_plus_UTRs_71mb.hg19.rm.bed is malformed: Problem reading the interval file caused by Badly formed genome loc: Contig 1 given as location, but this contig isn't present in the Fasta sequence dictionary ##### ERROR -----------------------------------------------------

[mak]

I had the same problem, my bed file looked like this:

1 position position
1 position position
1 position position
2 position position
...etc
while it should be:
chr1 position position
chr1 position position
chr1 position position
chr2 position position

a fix for this is:

cat bedfile.bed | sed 's:^:chr:'