Closed beginner984 closed 5 years ago
Your dropbox links do not work.
You are asking for a single read depth field for a breakpoint. There are two read depths for a breakpoint - one for each breakend. A SV can be homozygous at one breakend, and heterozygous at the other.
There are no standard VCF SV fields for your counts. Look at the VCF header for each of your callers. For delly could code will look like:
vcf = readVcf("delly.vcf")
tumour_pairs = geno(vcf)$DR
ref_pairs = geno(vcf)$DV
tumour_reads = geno(vcf)$RR
ref_reads = geno(vcf)$VR
Technically, a fragment can both a split read, and a discordant read pair and delly will double-count these fragments. GRIDSS gets corrects for this in it's VF
field. I'm not sure about manta.
Determining variant allele fraction from read depth at the location is technically incorrect: you want the coverage across the SV position
SV positions can be uncertain (IMPRECISE
VCF field). If you want to ignore all this, specify nominalPosition=TRUE
when calling breakpointRanges()
Driver is difficult to determine. I presume this is a cancer cohort. For cancer cohort analysis, I use the hartwig medical pipeline as it does SV + CN analysis well as detecting gene fusions, gene disruptions, and driver predictions. We should have a preprint on this pipeline available in about a mouth, but the pipeline is already complete (and successfully run on a 4,000 patient WGS cohort).
start/end positions can be extracted by:
vcf = readVcf("manta.vcf")
bpgr = breakpointRanges(vcf)
svbedpe_df = breakpointgr2bedpe(bpgr)
Note that for SVs, you also need to specify the orientation of the SV at the start/end positions. In this package, this is encoded in the strand of the GRanges object.
Note that the latest version of Delly is not VCF compliant and does not write both sides of BND
records as it is required to. I have not yet written code to handle these non-compliant SVs.
Thank you so much to be this much helpful, now links of .VCF files working
Actually I should find mutational signatures from SV data, so I called them but I don't know how to extract needed information from .VCF; another tool does mutational signature demands such a format
> head(svs.all[1:2,3:17])
Type Chrom1 Start1 End1 Strand1 Chrom2 Start2 End2 Strand2 Score Filters Read.pairs...tumour
1 BND chr3 25802405 25802858 + chr22 36811461 36812184 + 41 PASS 9
2 BND chr10 128580463 128581087 + chr18 25212086 25212571 + 44 PASS 5
Read.pairs...normal Split.reads...tumour Split.reads...normal
1 0 0 0
2 0 0 0
>
But I don't know how to get these columns from .VCF
another tool does mutational signature demands such a format
Which tool is this?
But I don't know how to get these columns from .VCF
Delly and manta store this information in different columns. Open the VCF files with a text edit and have a look at the header definitions.
E.g:
manta_split_read_count = geno(manta_vcf)$SR[,2]
Hi
I have called structural variants for tumour and matched normal samples by two software
Delly
andManta
; Now I have .vcf as output from which I want to extract such information but long time googling even contacting the developers failed for meTumor_Varcount = The number of variant bases at each position in tumour sample
This is my .vcf from delly
https://www.dropbox.com/s/4buzm8n7tebbyki/delly.vcf?dl=0
This is my .vcf from Manta
https://www.dropbox.com/s/a2mjlmeb1in3pms/candidateSV.vcf?dl=0
Any help please