tgong1

SV coordinates merged VCF from Manta and GRIDSS

3

Hi, I was merging VCFs from Manta and GRIDSS using SURVIVOR, while cannot understand many of the resulted SV coordintaes. Please see the following example (command: SURVIVOR merge sample_files 200...

Hi, (1) Are there any parameters can be used to change the threshold for the length of SV and indel events? (2) If I want to extract all variants in...

argument simulator_exectuable is required

2

Hi, I want to disable read simulation by using --disable_sim, but it still asked for simulator_exectuable path. Do you have any suggestions about this? Thank you, Tingting

All BNDs have no FORMAT:FT

6

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

SV in input VCF missed in graphtyper output VCF

2

Hi, I have used manta v1.6.0 for SV discovery and svimmer to create multi-sample VCF as the input for graphtyper v2.7.5 (graphtyper genotype_sv). I found some SVs in my input...

patients' phenotype -prostate cancer

2

Hi, Thank you for the useful software! We have SV data from prostate cancer patients. I'm wondering which phenotype I should include in column 6 of input when using Postre....

SV genotyping: Multiple BAMs for single sample

1

Dear author, Thank you for providing and maintaining this useful software. We have a question regarding SV genotyping using graphtyper. There are 10 samples in our cohort having two BAMs,...