Question: Use The Option -B/--Breakdancer For Pindel
0
gravatar for siyu
5.6 years ago by
siyu120
China
siyu120 wrote:

Pindel is able to use calls from other SV methods such as BreakDancer to further increase sensitivity and specificity. so when I use -b/--breakdancer when I run Pindel , there is a wrong :

pindel -f /rd/user/chengsj/CNV_detection/ref_genome/human_g1k_v37_modifyChr.fasta -i H9pindel.config -l -k -s -b h9.txt -Q H9_BD -c ALL -o H9

Pindel version 0.2.4t, August 13 2012.

something is wrong with this line "Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type"

Ignore breakdancer file due to an error in the BreakDancer file format.

the BreakDancer file format I use is like that :

*#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib H9x.bam

1 755514 19+17- 1 756372 19+17- INS -235 99 17 ../H9_merge_L3L4L5.bam.prefix.bam|17 NA

1 757510 6+7- 1 758272 6+7- DEL 57 64 5 ../H9_merge_L3L4L5.bam.prefix.bam|5 NA

1 774694 3+0- 1 775016 0+3- DEL 53 76 3 ../H9_merge_L3L4L5.bam.prefix.bam|3 0.52

1 797124 17+0- 1 797424 0+15- DEL 74 99 15 ../H9_merge_L3L4L5.bam.prefix.bam|15 2.03

does anyone have the problem??

breakdancer pindel • 2.1k views
ADD COMMENTlink modified 4.7 years ago by Biostar ♦♦ 20 • written 5.6 years ago by siyu120
0
gravatar for liangkaiye
5.6 years ago by
liangkaiye250
United States
liangkaiye250 wrote:

the breakdancer output file may be corrupted so that pindel ignores it. can you pass your file to me to analyze? kye@genome.wustl.edu

Kai

ADD COMMENTlink written 5.6 years ago by liangkaiye250
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