The target SV in *.svaba.sv.vcf is not found in *.alignments.txt.gz

[hhd1008611]

Hello, By the code: svaba run -t $TUM_BAM -t $NORM_BAM -p $CORES -k $k -a $name -G $REF I found the target SV in .svaba.sv.vcf, but the target SV is not found in .alignments.txt.gz. Is there something wrong with my code? Please tell me if this is normal, thank you very much.

[walaj]

I can’t see the whole SV, but if is a discordant-read only SV (DSCRD), it won’t be in alignments (contigs) file.

On Mon, Jul 31, 2023 at 10:30 AM hhd1008611 @.***> wrote:

Hello, By the code: svaba run -t $TUM_BAM -t $NORM_BAM -p $CORES -k $k -a $name -G $REF I found the target SV in .svaba.sv.vcf, but the target SV is not found in .alignments.txt.gz. Is there something wrong with my code? Please tell me if this is normal, thank you very much. [image: image] https://user-images.githubusercontent.com/35066896/257251221-f7206d3c-1fba-4b37-a690-f2437da5fcaf.png

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[hhd1008611]

Tanks for you reply, I checked the SV file according to what you said and found "EVDNC=DSCRD", chr5 49456740 319614841:1 T ]chr5:49471796]T 29 PASS DISC_MAPQ=60;EVDNC=DSCRD;IMPRECISE;MAPQ=60;MATEID=319614841:2;MATENM=-1;NM=-1;NUMPARTS=0;SCTG=chr5:49456740(-)-chr5:49471796(+)__57_49455501_49480501D;SPAN=15056;SVTYPE=BND GT:AD:DP:GQ:PL:SR:DR:LR:LO 0 0 12 0/1:12:35:29.9:29.9,0,56.3:0:12:-29.78:30.29 0/0:0:25:6.9:0,6.9,75.9:0:0:7.024:0 so next I want to delete the discordant-reads and then run SVaba, because the discordant-reads do not affect CNV, which I also cited with IGV. However, after deleting discordant-reads, *.svaba.sv.vcf found no SV, but there is clearly CNV from IGV. Something's wrong with my parameters or I don't have enough data? Here's my code:

samtools view -b -f3 -@ 12 $TUM_BAM  > $TUM_BAM_dediscordant
svaba run -t $TUM_BAM_dediscordant -p $CORES -k $k -a $name -G $REF

[hhd1008611]

The order of the IGV diagram is: first, $NORM_BAM second, $TUM_BAM third, $TUM_BAM_dediscordant

[walaj]

well the discordant reads are relevant for CNVs. What I think you mean is that they aren't substantial contributors to the copy-number. Svaba aims to compile rearrangement breakpoints, especially complex ones, that are most relevant in cancer genomes. For finding germline CNVs, you might try Lumpy