Header Problem with Picard

[ThomasWolf71]

Dear NGM developers and users,

i just tried NGM on my BAM files and it worked fine. But a problem occured when i tried to use Picard AddOrReplaceReadgroups on these BAM files. I got the following error message:

Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing SAM header. Problem parsing @PG key:value pair. Line: @PG ID: PN:ngm CL: --affine 0 --bam 1 --block_multiplier 2 --bs_cutoff 8 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast_pairing 0 --format 2 --gap_extend_penalty 5 --gap_read_penalty 20 --gap_ref_penalty 20 --gpu 1 { 0 } --hard_clip 0 --kmer 13

Seemingly the problems seem to arise from the "--" in all the header lines

Best regards Thomas

[ThomasWolf71]

Removed the -- entries from the header but now i still get the following error message Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing SAM header. Problem parsing @PG key:value pair. Line: @PG ID: PN:ngm CL: affine 0 bam 1 block_multiplier 2 bs_cutoff 8 bs_mapping 0 cpu_threads 4 dualstrand 1 fast_pairing 0 format 2

[ThomasWolf71]

VALIDATION_STRINGENCY=SILENT for AddOrReplaceReadGroups seems to offer a workaround to the problem. It would be really nice if NGM could add Read Groups to the generated BAM files.

[philres]

Hi Thomas,

thank you very much for your feedback. We will add the option to provide/add read group information in the next version of NextGenMap.

If you have any other suggestions don't hesitate to contact us.

Best, Philipp