mkirsche
commented
3 years ago Hi Chengcheng,
Thanks a lot for your interest in using Jasmine!
As for your first question, the best approach would be to have the distance thresholds depend on the length of the variants using the max_dist_linear parameter. While it doesn't explicitly look at overlap, it will give these large variants large distance thresholds so that they can be correctly merged with each other. I recommend something like this (though the exact values depend on the organism being studied and the upstream pipeline you are using): max_dist_linear=0.1 min_dist=50 --mutual_distance The --mutual_distance parameter was only added very recently to the Github build, so is not in the conda release yet if you are using that, but it will be added to conda in the next release later this week. Just to briefly explain the parameters:
max_dist_linear=0.1sets the distance threshold for each variant to 10% of its lengthmin_dist=50prevents the threshold from getting impossibly small for SVs of length below 100 or so by setting a lower bound of 50 on their distance threshold, so the threshold for each SV will be max(10% of length, 50)--mutual_distancerequires that for a pair of variants to be merged, they must both be within each other's distance threshold. By default, they only have to be within the larger of the two thresholds, which can be problematic for very large variants since they can end up merging with much smaller variants at similar genomic positions
For your second question, that format is correct. Jasmine can infer the length from the REF and ALT fields if they are filled out (so if they are e.g. A and ATGTATGCGT it will automatically use 9 as the SVLEN value). But if not, it falls back to the SVLEN field.
I hope that helps, and please don't hesitate to reach out with any other questions!
Best, Melanie
cai1991
Hi,
I'm trying your pipeline to merge my SVs, which were generated by whole genome comparisons among several de novo assemblies, into a single vcf file. I'm wondering:
C3 10180346 0_INV27953 N <INV> . PASS END=10361415;SVLEN=181069;SVTYPE=INV;AVG_LEN=181069.000000;AVG_START=10180346.000000;AVG_END=10361414.000000;SUPP_VEC_EXT=10;IDLIST_EXT=INV27953;SUPP_EXT=1;SUPP_VEC=10;SUPP=1;SVMETHOD=JASMINE;IDLIST=INV27953C3 10192856 1_INV34939 N <INV> . PASS END=10361415;SVLEN=168559;SVTYPE=INV;AVG_LEN=168559.000000;AVG_START=10192856.000000;AVG_END=10361414.000000;SUPP_VEC_EXT=01;IDLIST_EXT=INV34939;SUPP_EXT=1;SUPP_VEC=01;SUPP=1;SVMETHOD=JASMINE;IDLIST=INV34939C3 29342378 0_INV27963 N <INV> . PASS END=29948423;SVLEN=606045;SVTYPE=INV;AVG_LEN=606045.000000;AVG_START=29342378.000000;AVG_END=29948422.000000;SUPP_VEC_EXT=10;IDLIST_EXT=INV27963;SUPP_EXT=1;SUPP_VEC=10;SUPP=1;SVMETHOD=JASMINE;IDLIST=INV27963C3 29342378 1_INV34950 N <INV> . PASS END=29973346;SVLEN=630968;SVTYPE=INV;AVG_LEN=630968.000000;AVG_START=29342378.000000;AVG_END=29973345.000000;SUPP_VEC_EXT=01;IDLIST_EXT=INV34950;SUPP_EXT=1;SUPP_VEC=01;SUPP=1;SVMETHOD=JASMINE;IDLIST=INV34950C1 498768 INS37 N <INS> . PASS END=498768;ChrB=C1;StartB=496550;EndB=496651;Parent=SYN44;VarType=ShV;DupType=.;SVLEN=102;SVTYPE=INS;STRANDS=+Thank you very much in advance for your help.
Best regards, Chengcheng