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Understanding TRA in BEDPE output

See original GitHub issue

Hello,

I am trying to understand the TRA bedpe output.

Here are 3 examples:

#Chrom	start	stop	chrom2	start2	stop2	variant_name/ID	score (smaller is better)	strand1	strand2	type	number_of_supporting_reads	best_chr1	best_start	best_chr2	best_stop	predicted_length	FILTER
chr2L	0	-692077263	chr2L	136	0	21606	-1	-	+	TRA	6	chr3R	2254641	chrX	10411256	46018551	IMPRECISE
chr2L	0	-692077263	chr2L	136	0	21607	-1	+	+	TRA	2	chr3R	2259902	chrX	8866153	44468187	IMPRECISE
chr2L	0	18649216	chrY_CP007108v1_random	1901572213	0	21608	-1	+	-	TRA	2	chr3R	2270013	chrX	13159605	48751528	PRECISE

Here are the corresponding VCF entries:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT
chr3R	2254641	21606	N	]chrX:10411256]N	.	PASS	IMPRECISE;SVMETHOD=Snifflesv1.0.11;STD_quant_start=23.923489;STD_quant_stop=0.577350;Kurtosis_quant_start=1.184740;Kurtosis_quant_stop=0.000000;SVTYPE=BND;RNAMES=38d3ef42-c1f2-40ae-8b09-6525960cf573,598457ac-8685-472d-99ec-b6e6cf0456bb,97a926fa-c35f-4ac9-94a6-67850beaed5b,adbe8593-f6cd-4d6a-98d1-0d3584a68b3e,b2604ef5-54fd-432b-bac7-d081c36be068,d8593b1d-921f-43b0-9554-b9f996298b69;SUPTYPE=SR;SVLEN=0;STRANDS=-+;RE=6	GT:DR:DV	./.:.:6
chr3R	2259902	21607	N	N[chrX:8866153[	.	PASS	IMPRECISE;SVMETHOD=Snifflesv1.0.11;STD_quant_start=0.000000;STD_quant_stop=12.000000;Kurtosis_quant_start=-nan;Kurtosis_quant_stop=-2.000000;SVTYPE=BND;RNAMES=386b7d50-366e-42a3-a25c-ffe5b57aa733,6fe874ae-234b-4c61-a340-3a5260fc3c44;SUPTYPE=SR;SVLEN=0;STRANDS=++;RE=2	GT:DR:DV	./.:.:2
chr3R	2270013	21608	N	N[chrX:13159605[	.	PASS	PRECISE;SVMETHOD=Snifflesv1.0.11;STD_quant_start=7.516648;STD_quant_stop=0.000000;Kurtosis_quant_start=-1.982379;Kurtosis_quant_stop=-nan;SVTYPE=BND;RNAMES=a8926033-d473-422b-aece-ffad19897035,ca1e7475-277b-481c-94b8-c1fc491f77bc;SUPTYPE=SR;SVLEN=0;STRANDS=+-;RE=2	GT:DR:DV	./.:.:2

Here are the corresponding VCF entries with --report_BND:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT
chr3R	2254641	21606	N	<TRA>	.	PASS	IMPRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chrX;END=10411256;STD_quant_start=23.923489;STD_quant_stop=0.577350;Kurtosis_quant_start=1.184740;Kurtosis_quant_stop=0.000000;SVTYPE=TRA;RNAMES=38d3ef42-c1f2-40ae-8b09-6525960cf573,598457ac-8685-472d-99ec-b6e6cf0456bb,97a926fa-c35f-4ac9-94a6-67850beaed5b,adbe8593-f6cd-4d6a-98d1-0d3584a68b3e,b2604ef5-54fd-432b-bac7-d081c36be068,d8593b1d-921f-43b0-9554-b9f996298b69;SUPTYPE=SR;SVLEN=0;STRANDS=-+;RE=6	GT:DR:DV	./.:.:6
chr3R	2259902	21607	N	<TRA>	.	PASS	IMPRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chrX;END=8866153;STD_quant_start=0.000000;STD_quant_stop=12.000000;Kurtosis_quant_start=-nan;Kurtosis_quant_stop=-2.000000;SVTYPE=TRA;RNAMES=386b7d50-366e-42a3-a25c-ffe5b57aa733,6fe874ae-234b-4c61-a340-3a5260fc3c44;SUPTYPE=SR;SVLEN=0;STRANDS=++;RE=2	GT:DR:DV	./.:.:2
chr3R	2270013	21608	N	<TRA>	.	PASS	PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chrX;END=13159605;STD_quant_start=7.516648;STD_quant_stop=0.000000;Kurtosis_quant_start=-1.982379;Kurtosis_quant_stop=-nan;SVTYPE=TRA;RNAMES=a8926033-d473-422b-aece-ffad19897035,ca1e7475-277b-481c-94b8-c1fc491f77bc;SUPTYPE=SR;SVLEN=0;STRANDS=+-;RE=2	GT:DR:DV	./.:.:2

I guess I am really curious why Chrom start stop chrom2 start2 stop2 do not agree with best_chr1 best_start best_chr2 in the BEDPE output.

From the VCF output – it looks like maybe I should be ignoring the first 6 columns and only looking at the best stuff. Should I treat that as a generally true statement for types other than TRA as well?

Best,

John

p.s. I downloaded sniffles today to make sure I was working with the latest code.

Issue Analytics

State:
Created 5 years ago
Comments:6 (3 by maintainers)

Top GitHub Comments

1reaction

JohnUrbancommented, Feb 15, 2019

Hi Fritz – it looks like it is working as intended now. Here is the new BEDPE output that directly corresponds to the original bedpe/vcf outputs I provided:

chr3R   2254641 2254642 chrX    10411256        10411257        21606   -1      -       +       TRA     6       chr3R   2254641 chrX    10411256        46018551        IMPRECISE
chr3R   2259902 2259903 chrX    8866153 8866154 21607   -1      +       +       TRA     2       chr3R   2259902 chrX    8866153 44468187        IMPRECISE
chr3R   2270013 2270014 chrX    13159605        13159606        21608   -1      +       -       TRA     2       chr3R   2270013 chrX    13159605        48751528        PRECISE

Thanks again - I will close this assuming that would be your next move anyway.

0reactions

JohnUrbancommented, Feb 14, 2019

The soonest I will get to this is tomorrow - but I will be sure to let you know. Thanks.