Re: [Breakdancer-help] emty output bam2cfg.pl

[Ken C. <kc...@wa...>]

Are you trying to analyze SOLiD data?

-Ken

On 7/23/10 3:29 PM, Egor Clevac wrote:
> Egor Clevac
> Programmer, University of Pennsylvania.
> Phone Office: (215)-573-8776
>
>
> ----- Forwarded Message -----
> From: cl...@ma...
> To: bre...@li...
> Sent: Friday, July 23, 2010 4:06:12 PM GMT -05:00 US/Canada Eastern
> Subject: emty output bam2cfg.pl
>
> Hi,
> I am using breakdancer for the first time.
> Have trouble running bam2cfg.pl script, it gives me empty output.
>
> The header file of my bam file is:
> @HD	VN:1.0	GO:none	SO:coordinate
> @SQ	SN:chr1	LN:247249719
> @SQ	SN:chr2	LN:242951149
> @SQ	SN:chr3	LN:199501827
> @SQ	SN:chr4	LN:191273063
> @SQ	SN:chr5	LN:180857866
> @SQ	SN:chr6	LN:170899992
> @SQ	SN:chr7	LN:158821424
> @SQ	SN:chr8	LN:146274826
> @SQ	SN:chr9	LN:140273252
> @SQ	SN:chr10	LN:135374737
> @SQ	SN:chr11	LN:134452384
> @SQ	SN:chr12	LN:132349534
> @SQ	SN:chr13	LN:114142980
> @SQ	SN:chr14	LN:106368585
> @SQ	SN:chr15	LN:100338915
> @SQ	SN:chr16	LN:88827254
> @SQ	SN:chr17	LN:78774742
> @SQ	SN:chr18	LN:76117153
> @SQ	SN:chr19	LN:63811651
> @SQ	SN:chr20	LN:62435964
> @SQ	SN:chr21	LN:46944323
> @SQ	SN:chr22	LN:49691432
> @SQ	SN:chrX	LN:154913754
> @SQ	SN:chrY	LN:57772954
> @SQ	SN:chrM	LN:16571
> @RG	ID:P2L02	PL:Illumina	PU:02	SM:AU04404
> @PG	ID:GATK TableRecalibration	VN:1.0.3423	CL:Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate], default_read_group=null, default_platform=null, force_read_group=null, force_platform=null, solid_recal_mode=SET_Q_ZERO, window_size_nqs=5, homopolymer_nback=7, exception_if_no_tile=false, ignore_nocall_colorspace=false, pQ=5, maxQ=40, smoothing=1
>
>
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