Open ethering opened 6 months ago
Hi Graham, sorry for this. Do you see the ins in the VCF file ? Thanks Fritz
Hi Friz, Yes, they're at the end of the VCF file. Here are the VCF entries
Chr3 45180 INS1487952SURVIVOR N <INS> . LowQual PRECISE;SVTYPE=INS;SVMETHOD=SURVIVOR_sim;CHR2=Chr3;END=45341;SVLEN=161 GT:GL:GQ:FT:RC:DR:DV:RR:RV 1/1
Chr3 869844 INS1487955SURVIVOR N <INS> . LowQual PRECISE;SVTYPE=INS;SVMETHOD=SURVIVOR_sim;CHR2=Chr3;END=870223;SVLEN=379 GT:GL:GQ:FT:RC:DR:DV:RR:RV 1/1
Chr2 4354418 INS1487961SURVIVOR N <INS> . LowQual PRECISE;SVTYPE=INS;SVMETHOD=SURVIVOR_sim;CHR2=Chr2;END=4354910;SVLEN=492 GT:GL:GQ:FT:RC:DR:DV:RR:RV 1/1
Chr1 4982876 INS1487964SURVIVOR N <INS> . LowQual PRECISE;SVTYPE=INS;SVMETHOD=SURVIVOR_sim;CHR2=Chr1;END=4983124;SVLEN=248 GT:GL:GQ:FT:RC:DR:DV:RR:RV 1/1
Also, when I map real reads to the simulated reference with Minimap2, and use Sniffles to call SVs, I also get them reported in eval_simulated_right.vcf
ok that might be the best workaround for now. Sorry about this . Lately I was more focused on the VCF file than the fasta file.. Cheers Fritz
Hi, I'm running SURVIVOR v1.0.7 and I'm generating a simulated genome sequence with SVs in order to map my own reads to it and call SVs. First I'm generating a parameters file:
$ SURVIVOR simSV test_params.param
Output (I've increased the INDEL_value to ensure insertions):
Then I generated a simulated reference sequence (option 3=1) to generate the SVs:
So..... Sometimes when I run
SURVIVOR simSV
to generate the SVssimulated.insertions.fa
is totally empty, and sometimes it's not empty, but contains only the fasta header line of the insertions:I've run
SURVIVOR simSV
a number of times, using around 5 different param files (using different SV min/max sizes) and this behaviour is constant. However, when I run simSV with option 3=0, my insertions.fa file contains the insertions.Perhaps I've misunderstood something here, but intuitively I would presume that using option 3=1 (simulate genome), the insertions.fa would be the actual insertions in the simulated genome as using option3=0 (simulate reads), insertions.fa would be empty as the insertions are generated by
SURVIVOR simreads
which doesn't require the insertions.fa file.