[Breakdancer-help] emty output bam2cfg.pl

[Egor C. <cl...@ma...>]

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