I used tumor.bam and control.bam to call somatic SVs, but only can get SVs in control. The followings are my working process. Could you please tall me how can I solve this problem?
Then I used the following instruction to call SVs, but all SVs in tumor-normal.ctx are supported by reads only in normal.bam.
breakdancer-max -g SV_support_reads tumor-normal.cfg >tumor-normal.ctx
Why can't I get somatic SVs?
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I used tumor.bam and control.bam to call somatic SVs, but only can get SVs in control. The followings are my working process. Could you please tall me how can I solve this problem?
Generate tumor-normal.cfg
./bam2cfg.pl -g -h tumor.bam normal.bam >tumor-normal.cfg
The tumor-normal.cfg is this:
readgroup:1 platform:ILLUMINA map:tumor.bam readlen:95.32 lib:1 num:10001 lower:33.45 upper:356.94 mean:163.56 std:40.08 SWnormality:-49.69 flag:0(7.01%)1(0.10%)18(89.11%)2(1.03%)20(0.00%)32(1.63%)4(0.94%)8(0.16%)22438 exe:samtools view
readgroup:1 platform:ILLUMINA map:normal.bam readlen:97.26 lib:1 num:9998 lower:22.94 upper:382.58 mean:178.03 std:44.74 SWnormality:-41.16 flag:0(3.98%)1(0.17%)18(94.27%)2(0.58%)20(0.00%)32(0.38%)4(0.49%)8(0.12%)21206 exe:samtools view
Then I used the following instruction to call SVs, but all SVs in tumor-normal.ctx are supported by reads only in normal.bam.
breakdancer-max -g SV_support_reads tumor-normal.cfg >tumor-normal.ctx
Why can't I get somatic SVs?
Any progress on this issue? I have the same problem.