All BNDs have no FORMAT:FT

[tgong1]

Hi,

There are no FT tags in FORMAT fields for ALL BNDs. Do you have any idea why this happen?
Any idea or suggestion is appreciated.

Thank you,
Tingting

[tgong1]

Hi, I also found all BNDs have only AGGREGATED models. Is this what expected to see? I have used Manta for calling and svimmer for SV merging.

Thank you,
Tingting

[jingydz]

Hi, do you have solved this problem?
I meet the same problem.
normal SV type, such as DEL, INS, DUP, all have FT field
but BND no FT field, before vcffillter -g FT=PASS

after vcffilter -g FT=PASS

all sample genotype of BND changed from 0/0 or 0/1 into "."，that 's true？

[tgong1]

Hi,

No, I haven't solve the problem of BND. So I have given up the method of filtering based on FT=PASS. I'm now using the PASS_ratio for filtering.

Best regards,
Tingting

[jingydz]

BND：-f "( SVTYPE = BND & QD > 20 & ( ABHet > 0.30 | ABHet < 0 ) & ( AC / NUM_MERGED_SVS ) < 10 & PASS_AC > 0 & PASS_ratio > 0.1 )"

-f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter

-g, --genotype-filter specifies a filter to apply to the genotype fields of records

If you only use the PASS_ratio, then it only filter the BND records but not sample genotype? can it filter unpassed genotype?

[tgong1]

@jingydz Yes, the filtering I'm using now is for SV sites only. While I have also tried on filtering BND based on GQ>40 (you have to set a threshold here), and other types based on FT=PASS. Hope that helps.

[jingydz]

Thank you again. Finally I used "( GQ > 20 ) & ( AD > 10 )" for BND and "FT=PASS" for other types.