Example SV VCF file

[Alex-Nesta]

Hi, would you please upload an example VCF file that contains exactly what the program is looking for when it is reading an SV from LUMPY?

So far, I have run LUMPY on my samples, sorted (lsort) and merged (lmerge) using svtools. Once I sort and merge, there is no longer a separate column for each sample genotype. Instead, the sample ID is in column 8 in the ";" separated list.

Does your modified code handle this properly?

I tried running your modified program using one sample genotype per column (as fastQTL traditionally handles SNVs), but it returned NAs for the result. I assume this is because fastQTL failed to properly read the VCF with SVs in it.

An example VCF would really clear up a lot of confusion for me.

Thanks,
Alex

[Alex-Nesta]

Update: it appears the modified fastqtl is still looking for a separate column for each sample ID.
still working on this. I will try to post if I get a working example vcf.

[Alex-Nesta]

Just another update, I managed to get DUPs and DELs recognized properly (I think) by this fastQTL fork.

Essentially, I used lumpy-express to call SVs, and then I genotyped the SVs. Multiple samples were sorted and merged using vcf-tools.

Aside: Using the l_sort and l_merge scripts would probably be preferred over vcf-tools, because they allow you to combine SVs where the breakpoints are essentially on top of each other, eliminating duplicate calls. Problem is that the lumpy tools combine sample IDs into column 8, and I haven't written a script to separate each sample into columns yet.

Note that column 8 contains the END and SVTYPE identifiers. Each sample column (10 and +) has the genotype (GT) data as described in column 9. The probability data (PRPOS) was required to call genotypes, see lumpy-sv docs for more info.

I'll update once I get BNDs to work.

Here is what the line looks like:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample10	Sample12	Sample13	Sample14	Sample15	Sample16	Sample17	Sample18	Sample19	Sample20	Sample21	Sample22	Sample23	Sample24	Sample2	Sample3	Sample4	Sample5	Sample6	Sample7	Sample8	Sample9
chr1	859750	252	N	<DEL>	4.77	.	AC=0;AN=2;CIEND95=-1,4;CIEND=-1,5;CIPOS95=-3,27;CIPOS=-10,51;END=859862;IMPRECISE;PE=5;PREND=0.270669,0.289457,0.210011,0.119331,0.0592752,0.0302291,0.0142419;PRPOS=1.7852e-05,4.15862e-05,9.60167e-05,0.000221446,0.000525034,0.00124281,0.00285498,0.0065645,0.015134,0.0356146,0.0832676,0.0762724,0.06883,0.0639363,0.0590887,0.0544545,0.0500409,0.0458164,0.0420522,0.0388982,0.0354741,0.0323669,0.0294378,0.0267039,0.0244704,0.0220437,0.020198,0.017996,0.0165371,0.0149417,0.0132844,0.0120834,0.0107603,0.00961301,0.00867336,0.00762267,0.00689714,0.00622135,0.00541836,0.00476669,0.00424522,0.00378864,0.0033862,0.00292853,0.0025243,0.00219774,0.00194794,0.00167578,0.00143237,0.00114525,0.000918337,0.000776454,0.000638936,0.000510444,0.000401923,0.000308642,0.00022872,0.000174399,0.000117129,8.53343e-05,5.4326e-05,2.48802e-05;SF=9;SR=0;STRANDS=+-:5;SU=5;SVLEN=-112;SVTYPE=DEL	GT:QA:AP:PE:SQ:RP:RO:RS:GL:AB:QR:GQ:SU:DP:AO:ASC:AS:SR	.	.	.	.	.	.	.	.	.	0/0:0:0:5:4.77:0:0:0:0,0,0:.:0:0:5:0:0:0:0:0	.	.	.	.	.	.	.	.	.	.	.	.
chr1	860295	519	N	<DEL>	80.91	.	AC=1;AN=2;CIEND95=-34,3;CIEND=-146,9;CIPOS95=-3,53;CIPOS=-10,186;END=860634;IMPRECISE;PE=5;PREND=3.36997e-10,9.94146e-10,2.40071e-09,4.16405e-09,6.49299e-09,1.03638e-08,1.61741e-08,2.46637e-08,3.23112e-08,4.0074e-08,5.07844e-08,6.52929e-08,8.41545e-08,1.05265e-07,1.27189e-07,1.5477e-07,1.78854e-07,2.08976e-07,2.50998e-07,3.04131e-07,3.69321e-07,4.46373e-07,5.33338e-07,6.27191e-07,7.24286e-07,8.308e-07,9.30538e-07,1.0682e-06,1.22085e-06,1.39513e-06,1.57983e-06,1.8082e-06,2.03635e-06,2.28963e-06,2.52443e-06,2.84861e-06,3.19468e-06,3.58949e-06,4.04572e-06,4.57181e-06,5.16105e-06,5.77701e-06,6.41157e-06,7.19474e-06,8.06504e-06,8.98735e-06,1.00585e-05,1.10021e-05,1.20583e-05,1.34856e-05,1.47488e-05,1.60243e-05,1.7597e-05,1.96317e-05,2.13581e-05,2.3401e-05,2.56325e-05,2.82434e-05,3.10602e-05,3.38598e-05,3.73457e-05,4.16437e-05,4.53932e-05,4.98154e-05,5.50491e-05,5.97549e-05,6.54644e-05,7.18418e-05,7.89633e-05,8.65266e-05,9.47819e-05,0.000103832,0.000113182,0.000124134,0.000136036,0.000149681,0.000165045,0.000180943,0.000196764,0.000213369,0.000231585,0.000255511,0.000281664,0.000308902,0.000339463,0.000371575,0.00040776,0.000448737,0.000491027,0.000532373,0.000581073,0.00063343,0.000686291,0.00074709,0.000822449,0.000892383,0.000979753,0.00107627,0.00118016,0.00129532,0.00141807,0.00155181,0.00170886,0.00188032,0.00208042,0.00231185,0.00253665,0.00277465,0.00304439,0.00333359,0.00363924,0.00397084,0.00430616,0.00467177,0.00513529,0.00559597,0.00609761,0.00669258,0.00732843,0.00797467,0.00870626,0.00948106,0.0103493,0.0112998,0.0123916,0.013579,0.0148483,0.0161297,0.0174798,0.0190158,0.0206354,0.0223011,0.0240289,0.0260776,0.0284105,0.0309756,0.0335473,0.0361875,0.0391871,0.0424961,0.0460604,0.0498805,0.0540045,0.0584094,0.0633949,0.0685354,0.0741142,0.0318123,0.0135986,0.00577576,0.00245155,0.00103849,0.000439818,0.000186502,7.89387e-05,3.34193e-05;PRPOS=7.14067e-06,1.72892e-05,4.17462e-05,0.000100757,0.000243395,0.000588548,0.00142225,0.0034394,0.00831273,0.0200909,0.0485244,0.0460796,0.0437334,0.0415605,0.0395235,0.0376101,0.0359061,0.0342495,0.0327092,0.0311547,0.0296639,0.0281581,0.026648,0.0253474,0.0240968,0.0228779,0.0218041,0.0207625,0.0198358,0.0188997,0.0179145,0.0170128,0.0161385,0.0153311,0.0145524,0.0138764,0.013148,0.0125067,0.0118841,0.0112997,0.0106916,0.010094,0.00953455,0.00899931,0.00852589,0.00806857,0.00766014,0.00727668,0.00690763,0.00654466,0.00615401,0.00578925,0.00547308,0.00515611,0.00487162,0.00459615,0.00435319,0.00412744,0.00391398,0.00370404,0.00350748,0.00332051,0.00313278,0.00295301,0.00277424,0.00263529,0.00249186,0.00237068,0.00224772,0.00212328,0.00201193,0.00189792,0.00177889,0.00166944,0.0015682,0.00147132,0.00138547,0.00130459,0.00123074,0.00116206,0.00109174,0.00103212,0.00097557,0.000914163,0.000857913,0.000806468,0.00075509,0.000707856,0.00066365,0.000624744,0.000587666,0.000553879,0.000518118,0.000483485,0.00045303,0.000423176,0.000395661,0.000371725,0.000347902,0.000323621,0.000303179,0.0002841,0.000266282,0.000247926,0.000230858,0.000215708,0.000202541,0.00018908,0.000177176,0.000166031,0.000155765,0.000145074,0.000135522,0.000126739,0.000117621,0.000109935,0.000102201,9.55954e-05,9.01875e-05,8.42025e-05,7.82428e-05,7.31522e-05,6.80125e-05,6.32902e-05,5.90287e-05,5.53681e-05,5.19025e-05,4.82196e-05,4.51652e-05,4.18543e-05,3.89894e-05,3.62893e-05,3.39891e-05,3.17897e-05,2.93895e-05,2.73256e-05,2.54582e-05,2.34763e-05,2.18131e-05,2.02338e-05,1.867e-05,1.73542e-05,1.61722e-05,1.50073e-05,1.40912e-05,1.30026e-05,1.21609e-05,1.12981e-05,1.03512e-05,9.50993e-06,8.84863e-06,8.15705e-06,7.5798e-06,6.94639e-06,6.46596e-06,5.93088e-06,5.43546e-06,4.98604e-06,4.55111e-06,4.11931e-06,3.79024e-06,3.46272e-06,3.15813e-06,2.90864e-06,2.65818e-06,2.42833e-06,2.2466e-06,2.03065e-06,1.84844e-06,1.69123e-06,1.51416e-06,1.39194e-06,1.28027e-06,1.15755e-06,1.05081e-06,9.46694e-07,8.38378e-07,7.45964e-07,6.52033e-07,5.81355e-07,5.1363e-07,4.72223e-07,4.19293e-07,3.72038e-07,3.25425e-07,2.85187e-07,2.43389e-07,2.15842e-07,1.85914e-07,1.67506e-07,1.36357e-07,1.07857e-07,8.37692e-08,6.68153e-08,5.3479e-08,3.80677e-08,2.24177e-08;SF=11;SR=0;STRANDS=+-:5;SU=5;SVLEN=-339;SVTYPE=DEL	GT:RS:QR:AB:GL:ASC:AS:AO:DP:SU:GQ:SR:AP:QA:SQ:PE:RP:RO	.	.	.	.	.	.	.	.	.	.	.	0/1:0:9:0.31:-9,-1,-6:0:0:4:14:5:52:0:4:4:80.91:5:9:9	.	.	.	.	.	.	.	.	.	.
chr1	877320	204	N	<DEL>	0.01	.	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chr1	877383	520	N	<DEL>	0.26	.	AC=0;AN=2;CIEND95=-14,2;CIEND=-17,9;CIPOS95=-3,36;CIPOS=-10,59;END=877619;IMPRECISE;PE=4;PREND=0.00368647,0.00626487,0.0106152,0.0147288,0.0181077,0.0222881,0.0285659,0.0352719,0.0431634,0.0472847,0.0540224,0.0603227,0.0699851,0.0783219,0.0892919,0.0987404,0.109461,0.118123,0.0516624,0.0224179,0.00997902,0.00435291,0.00191117,0.000828423,0.000357207,0.000153503,6.4794e-05;PRPOS=1.10627e-05,2.64122e-05,6.25857e-05,0.000148894,0.000352602,0.000846284,0.00202241,0.00481324,0.0114567,0.0271961,0.06423,0.0603025,0.056413,0.0527411,0.049726,0.0467756,0.0438041,0.0412651,0.0381695,0.0360464,0.0337639,0.0315422,0.0294323,0.0277134,0.025726,0.0242496,0.0224528,0.0210624,0.0194948,0.018183,0.0168799,0.0156658,0.0143599,0.0133316,0.0123877,0.0114745,0.010677,0.00996885,0.00923464,0.0085662,0.00789743,0.00731814,0.0068001,0.00621301,0.00580163,0.00543753,0.00503937,0.00463878,0.00424678,0.00385693,0.00352466,0.00313308,0.00285748,0.00258962,0.00241773,0.00219864,0.00198982,0.00178072,0.00160908,0.00139195,0.00125542,0.00110404,0.00100759,0.000826473,0.000669014,0.000532107,0.000433304,0.000352228,0.000257061,0.000153711;SF=11;SR=0;STRANDS=+-:4;SU=4;SVLEN=-236;SVTYPE=DEL	GT:RP:RO:SQ:PE:AP:QA:SR:SU:DP:GQ:ASC:AS:AO:GL:AB:QR:RS	.	.	.	.	.	.	.	.	.	.	.	0/0:22:22:0.26:4:2:2:0:4:25:12:0:0:2:-4,-5,-20:0.083:22:0	.	.	.	.	.	.	.	.	.	.```

[netwon123]

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