Hi~ I am pretty new to this area, having a hard time with these huge files..
I wanted to use IndelGenotyperV2 (from GATK) with my newly built BAM files. When I executed the command I found an error like below..
java.lang.RuntimeException: net.sf.samtools.SAMFormatException: Error parsing SAM header. Problem parsing @PG key:value pair.
And the @PG line is like below:
@PG ID:illumina_export2sam.pl VN:2.0.0 CL:/opt/GOAT/CASAVA_1.7.0a6/bin/illumina_export2sam.pl --read1=s_7_1_export.txt --read2=s_7_2_export.txt
I don't figure out what the problem is here.. There are all three tags (ID, VN, and CL).
One hint is that I can find a warning when I check the header part with samtools (samtools view myfile.bam -H) like below:
The tag '--' present (at least) twice on line [@PG ID:illumina_export2sam.pl VN:2.0.0 CL:/opt/GOAT/CASAVA_1.7.0a6/bin/illumina_export2sam.pl --read1=s_7_1_export.txt --read2=s_7_2_export.txt]
Is this a cause of this error? or there's any other problem in my file?
Thanks,
I wanted to use IndelGenotyperV2 (from GATK) with my newly built BAM files. When I executed the command I found an error like below..
java.lang.RuntimeException: net.sf.samtools.SAMFormatException: Error parsing SAM header. Problem parsing @PG key:value pair.
And the @PG line is like below:
@PG ID:illumina_export2sam.pl VN:2.0.0 CL:/opt/GOAT/CASAVA_1.7.0a6/bin/illumina_export2sam.pl --read1=s_7_1_export.txt --read2=s_7_2_export.txt
I don't figure out what the problem is here.. There are all three tags (ID, VN, and CL).
One hint is that I can find a warning when I check the header part with samtools (samtools view myfile.bam -H) like below:
The tag '--' present (at least) twice on line [@PG ID:illumina_export2sam.pl VN:2.0.0 CL:/opt/GOAT/CASAVA_1.7.0a6/bin/illumina_export2sam.pl --read1=s_7_1_export.txt --read2=s_7_2_export.txt]
Is this a cause of this error? or there's any other problem in my file?
Thanks,
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