Sample names with spaces are not supported

[ernfrid]

I have unfortunately encountered a CRAM file with an SM field within the @rg lines containing a space. I believe this is valid according to the BAM specification.

When running lumpyexpress on this file the resulting VCF truncates the sample name at the space.
For example, the line:

@RG	ID:2895621816	CN:WUGSC	LB:lib1	PL:ILLUMINA	PU:XXXXXX.X	SM:SAMPLE -50

would result in a VCF containing the sample SAMPLE instead of SAMPLE -50.

[ryanlayer]

Would it be okay if I convert the " " to a "_"? Can you email me this bam with 1/2 million alignments?

…

On Fri, Jul 21, 2017 at 2:32 PM, Dave Larson ***@***.***> wrote: I have unfortunately encountered a file with an SM tag containing a space. I believe this is valid. When running lumpyexpress on this file the resulting VCF truncates the sample name at the space. For example, the tag: @rg ID:2895621816 <(289)%20562-1816> CN:WUGSC LB:lib1 PL:ILLUMINA PU:XXXXXX.X SM:SAMPLE -50 would result in a VCF containing the sample SAMPLE instead of SAMPLE -50. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#199>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAlDUQ6t-PrEYWVSHTgHwA-l2TmpcLXBks5sQQragaJpZM4Of3K6> .

-- Ryan Layer

[ernfrid]

I think converting a space to an underscore would just put me in the same position I'm in now, a different sample name in the output file and poor interaction with tools that handle the sample name properly.

Unfortunately, this is protected access data and thus, I can't share.

[ryanlayer]

Can you send me the command that lumpyexpress tries to run? I was thinking that it may work if the -pe and -sr options could be encased in the double quotes.

[ernfrid]

Here's what is printed in the log file.

/opt/lumpy-sv//bin/lumpy -P \
    -t H_TK-D240629_-50-D240629_-50.lumpy.temp/H_TK-D240629_-50-D240629_-50.vcf.tmp \
    -msw 4 \
    -tt 0 \
     \
    -x /gscmnt/gc2802/halllab/ccdg_resources/genomes/human/GRCh38DH/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed \
     -pe bam_file:H_TK-D240629_-50-D240629_-50.discordants.bam,histo_file:H_TK-D240629_-50-D240629_-50.lumpy.temp/H_TK-D240629_-50-D240629_-50.vcf.tmp.sample1.lib1.x4.histo,mean:364.530025182,stdev:80.5523897695,read_length:151,min_non_overlap:151,discordant_z:5,back_distance:10,weight:1,id:D240629,min_mapping_threshold:20,read_group:2895621640,read_group:2895621762,read_group:2895621763,read_group:2895621774,read_group:2895621775,read_group:2895621809,read_group:2895621810,read_group:2895621816 \
     -sr bam_file:H_TK-D240629_-50-D240629_-50.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:D240629,min_clip:20 \
    > H_TK-D240629_-50-D240629_-50.vcf.tmp

[ernfrid]

I don't have the temp directory preserved, but I can rerun if that would help.

[ernfrid]

@ryanlayer - I think I may have a solution to this (#208) but I've not tested extensively and my bash is pretty weak. Let me know if you see any issues with what I put together.