Open jingydz opened 9 months ago
The reference SV sets of NA12878 and NA19240 to be used for the evaluation of SV detection tools (used for Fig. 2 and Figs. S1-S7) are GRCh37-based ones. As described in Methods of the paper, the NA12878 reference SV set was generated by combining the DGV variant data (2016-05-15 version) with long read-based SVs (Pendelton et al., Nat Methods 2015) without redundancy. For the NA19240 reference SV set, the DGV variants (2016-05-15 version) was combined with nstd152.GRCh37.variant_call.vcf.gz obtained at the NCBI dbVar site, which contained >= 30 bp variants.
Could you please share the finally reference SV sets of NA12878 and NA19240? Thank you in advance.
The NA19240 reference sv vcf file was uploaded at https://github.com/stat-lab/EvalSVcallers/tree/master/Ref_SV. The reference vcf for NA12878 is NA12878_DGV-2016_LR-assembly.vcf at that site.
Are both of these files (NA19240.nstd152.DGV.GRCh37.sv.min30.vcf, NA12878_DGV-2016_LR-assembly.vcf) based on GRCh37? If I need GRCh38, do I need to convert them to GRCh38?
In your paper, you wrote:"The reference SVs for NA19240 (38,562) contained 1.5-fold more SVs than the reference SVs for NA12878 (25,736), probably due to the remaining redundant SVs in the HGSV data."
I checked the vcf file. $ zcat NA19240.nstd152.DGV.GRCh37.sv.min30.vcf.gz |wc -l 40961 $ zcat NA12878_DGV-2016_LR-assembly.vcf.gz |wc -l 25812
Could you tell me what processing you did afterwards to obtain the number mentioned in the paper?
Sorry for your confusion. The number of SV is that after filtering of > 2 Mb DELs/DUPs/INVs and DELs/DUPs overlapping with the GRCh37 gap regions, because our evaluation script removes these filtered variants from the reference SVs on evaluation (see https://github.com/stat-lab/EvalSVcallers/blob/master/scripts/evaluate_SV_callers.pl).
Hi,
I filtered the two files you provided according to your instructions, but why am I still not getting the same numbers? (except for INS).
Hi, I want to know what files are the real SV datasets of NA12878 and NA19240 finally? And which one is GRCh38 version?
In your paper, you wrote:"The reference SVs for NA19240 (38,562) contained 1.5-fold more SVs than the reference SVs for NA12878 (25,736), probably due to the remaining redundant SVs in the HGSV data."
I downloaded the HGSGV data "variants_freeze4_sv_insdel_alt.vcf.gz". And $ bcftools view -s NA19240 --exclude-uncalled --threads 10 variants_freeze4_sv_insdel_alt.vcf.gz -Oz -o hgsvc.NA19240.vcf.gz $ zcat hgsvc.NA19240.vcf.gz |grep -v "^#" |grep -v "0|0" |wc -l 30630
I found NA19240 only had 20394 SVs, and HGSVC dataset only have INS and DEL, no other SV types.
$ bcftools view -s NA12878 --exclude-uncalled --threads 10 variants_freeze4_sv_insdel_alt.vcf.gz -Oz -o hgsvc.NA12878.vcf.gz $ zcat hgsvc.NA12878.vcf.gz |grep -v "^#" |grep -v "0|0" |wc -l 27538
In addition, I downloaded https://github.com/stat-lab/EvalSVcallers/blob/master/Ref_SV/NA12878_DGV-2015_LR-assembly.vcf and https://github.com/stat-lab/EvalSVcallers/blob/master/Ref_SV/NA12878_DGV-2016_LR-assembly.vcf
$ zcat NA12878_DGV-2015_LR-assembly-maybeHG19.vcf.gz |wc -l 24736
$ zcat NA12878_DGV-2016_LR-assembly-maybeHG38.vcf.gz |wc -l 25812
I noticed that these numbers don't match the ones you provided earlier. Can you please be more specific about how you processed them?