Know SV can not detected by manta

[iskysinger]

Hi all,
I have a bam file with the reads with the breakpoint chr:186356039, but it didn't detect by manta (No such breakpoint in candidateSV.vcf ), below are the reads from the bam file. Any people have experience with this situation. Thanks a lot.

A01516:26:H577TDSX3:3:2360:3432:21590	0	chr1	186356039	60	48S107M	*	0	0	CCAAAGTCAGTCATCAGAGGAGTCCCATGACTCCCAGGAATTGGCCTGATAACCAAAATAAATACTGTAATTCATTGATTCTGTAATGCACCTTTTTCAACAATAGAAAGCATTTCTTTTTAGCAATACATAAAATAATGGTATGTTTTACAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF	NM:i:1	MD:Z:35A71	AS:i:102	XS:i:21	RG:Z:TW-5-50ngCol2	SA:Z:chr2,29224030,+,48M107S,60,0;
A01516:26:H577TDSX3:4:1250:1127:3881	0	chr1	186356039	60	40S106M	*	0	0	AGTCATCAGAGGAGTCCCATGACTCCCAGGAATTGGCCTGATAACCAAAATAAATACTGTAATTCATTGATTCTGAAATGCACCTTTTTCAACAATAGAAAGCATTTCTTTTTAGCAATACATAAAATAATGGTATGTTTTACAGT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF::FF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFF:FF:F,FF:FFFFFFF:::FF	NM:i:0	MD:Z:106	AS:i:106	XS:i:20	RG:Z:TW-5-50ngCol2	SA:Z:chr2,29224038,+,40M106S,60,0;
A01516:26:H577TDSX3:3:2360:3432:21590	16	chr1	186356039	60	30S119M6S	*	0	0	GGAGTCCCATGACTCCCAGGAATTGGCCTGATAACCAAAATAAATACTGTAATTCATTGATTCTGAAATGCACCTTTTTCAACAATAGAAAGCATTTCTTTTTAGCAATACATAAAATAATGGTATGTTTTACAGTTGATGGGATGTTACGTATC	FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:F:FF,F:FFFF,FFF:FF::FFFFFFFFFFFF,FFFFFFFFFFF:,FFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF	NM:i:0	MD:Z:119	AS:i:119	XS:i:20	RG:Z:TW-5-50ngCol2	SA:Z:chr2,29224048,-,30M125S,60,0;
A01516:26:H577TDSX3:4:1250:1127:3881	16	chr1	186356039	60	27S117M5S	*	0	0	GTCCCATGACTCCCAGGAATTGGCCTGATAACCAAAATAAATACTGTAATTCATTGATTCTGAAATGCACCTTTTTCAACAATAGAAAGCATTTCTTTTTAGCAATACATAAAATAATGGTATGTTTTACAGTTGATGGGATGTATCGG	:FFFF,:F:FFFFFFF::F:,FFFFFFFFFFFFF:,::FF,,,FFFFF,F:FF:FFFFFFFFFFFFFFFFF:F::FFFFF:,FFFF::FFF:FFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:117	AS:i:117	XS:i:20	RG:Z:TW-5-50ngCol2

[Cassiel60]

Hello ,
I have the same question now, I have tried to modify the parameters ,but it still not resolved . how do you resolve it ?

[iskysinger]

@Cassiel60 I tried all the different parameters, but still can't detect the SV I expected. Not sure how that happened.

[esamorodnitsky]

I am having a similar issue. If anyone can tell me anything about this, please let me know!