Manta cannot detect same chromosome large deletions

[jdzdroid]

Hi,

I generated test cases and was trying to detect large deletions within the same chromosomes and found that manta wasn't calling them. Viewing in IGV the gaps are visible. Translocations from chr17 to chr22 is also in the testcase and is being called correctly. Thanks for your help and let me know if you need any additional information.

manta_large_del.tar.gz

[QuanlongJiang]

I also got this problem. Large deletion or inversion in the same chromosome can't be detected. Have you solved this?

[Solenyalyl]

I also got this problem,any suggestions?

[mvheetve]

Hi,

we used Manta for SV calling on WGS data (30-40x). Two cases should have large deletions as already picked up by other sequencing and PCR efforts, but neither of those can be found in the Manta files (candidate SV files or final diploid file). For case 1 (homozygous deletion chr16:75457433-75510060) we see a lack of reads in the IGV track, consistent with the expected deletion. For case 2 (heterozygous deletion chrX:154097604-154154739) we see reduction of coverage in the expected region.

Could the authors please comment on this issue? I'm not able to share the data, but I will be as supportive as possible in order to help fix this issue.

Regards Mattias

[QuanlongJiang]

I‘ve switched to lumpy. Gridss2 is also OK. The sensitivity is not good of Manta. I'm not sure it's easy to solve.

[Solenyalyl]

I found my solution,I have set target bed file,when drop this parameter,we got the large deletions and translocations

---- Replied Message ---- | From | @.> | | Date | 08/12/2022 23:04 | | To | @.> | | Cc | @.@.> | | Subject | Re: [Illumina/manta] Manta cannot detect same chromosome large deletions (#255) |

Hi,

we used Manta for SV calling on WGS data (30-40x). Two case should have large deletions as already picked up by other sequencing and PCR efforts, but neither of those can be found in the Manta files (candidate SV files or final diploid file). For case 1 (homozygous deletion chr16:75457433-75510060) we see a lack of reads in the IGV track, consistent with the expected deletion. For case 2 (heterozygous deletion chrX:154097604-154154739) we see reduction of coverage in the expected region.

Could the authors please comment on this issue? I'm not able to share the data, but I will be as supportive as possible in order to help fix this issue.

Regards Mattias

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[QuanlongJiang]

I found my solution,I have set target bed file,when drop this parameter,we got the large deletions and translocations … ---- Replied Message ---- | From | @.> | | Date | 08/12/2022 23:04 | | To | @.> | | Cc | @.@.> | | Subject | Re: [Illumina/manta] Manta cannot detect same chromosome large deletions (#255) | Hi, we used Manta for SV calling on WGS data (30-40x). Two case should have large deletions as already picked up by other sequencing and PCR efforts, but neither of those can be found in the Manta files (candidate SV files or final diploid file). For case 1 (homozygous deletion chr16:75457433-75510060) we see a lack of reads in the IGV track, consistent with the expected deletion. For case 2 (heterozygous deletion chrX:154097604-154154739) we see reduction of coverage in the expected region. Could the authors please comment on this issue? I'm not able to share the data, but I will be as supportive as possible in order to help fix this issue. Regards Mattias — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

But I never used target bed.

[mvheetve]

I found my solution,I have set target bed file,when drop this parameter,we got the large deletions and translocations … ---- Replied Message ---- | From | @.> | | Date | 08/12/2022 23:04 | | To | _@**._> | | Cc | _@.@._> | | Subject | Re: [Illumina/manta] Manta cannot detect same chromosome large deletions (#255) | Hi, we used Manta for SV calling on WGS data (30-40x). Two case should have large deletions as already picked up by other sequencing and PCR efforts, but neither of those can be found in the Manta files (candidate SV files or final diploid file). For case 1 (homozygous deletion chr16:75457433-75510060) we see a lack of reads in the IGV track, consistent with the expected deletion. For case 2 (heterozygous deletion chrX:154097604-154154739) we see reduction of coverage in the expected region. Could the authors please comment on this issue? I'm not able to share the data, but I will be as supportive as possible in order to help fix this issue. Regards Mattias — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: _@_.*>

But I never used target bed.

Same for me, I never set a targeted bed file.