question: how was filter of delly calls performed and decided upon?

[anoronh4]

We recently accessed several of the pcawg variant calls and realized that based on the name of the files, it was likely that the delly filter step was being omitted, since the naming pattern was <id>.embl-delly_<version>-preFilter.<date>.somatic.sv.vcf.gz. we were just wondering the reason for this, and how pcawg filters the calls before merging them with other callers.

we did notice that the script DellySomaticFreqFilter.py exists in this repo, but were curious to know why any *highConf.vcf were left out of the shared pcawg SV calls, and why the workflow deviated from the built in delly filter algorithm. also, any guidance on how to build the PoN for delly calls?

[anoronh4]

i did give the script DellySomaticFreqFilter.py a try for the unfiltered vcf calls that we downloaded from pcawg, and found it strange that i got a such a wide range proportions of vcf records that were kept. i'm wondering now if there's some feature in some of the vcf files (DO1015_tumor__DO1015_normal for example) that would cause variants to be incorrectly skipped. below is the table of counts:

id	original number of rows	number of rows after filtering	proportion	pcawg vcf file prefix
DO1015_tumor__DO1015_normal	432	0	0	f393bb08-5b50-e009-e040-11ac0d484537.embl-delly_1-0-0-preFilter.20150618
DO218709_tumor__DO218709_normal	368	0	0	fc8130e0-0f1a-b6eb-e040-11ac0c48328f.embl-delly_1-0-0-preFilter.20150614
DO220878_tumor__DO220878_normal	189	0	0	9fc5b5c7-3973-42b4-8710-454de0cb5b50.embl-delly_1-0-0-preFilter.20150730
DO32960_tumor__DO32960_normal	131	0	0	b37d6283-6f95-4975-a794-f3d5c4bbc7b3.embl-delly_1-0-0-preFilter.20150705
DO45239_tumor__DO45239_normal	684	0	0	d182b67c-c622-11e3-bf01-24c6515278c0.embl-delly_1-0-0-preFilter.20150712
DO51533_tumor__DO51533_normal	160	0	0	d1804679-e728-4597-ac69-49554c087b9e.embl-delly_1-0-0-preFilter.20150722
DO6580_tumor__DO6580_normal	95	0	0	c642b9cc-bdb1-4796-9692-8be92398be17.embl-delly_1-0-0-preFilter.20150604
DO220885_tumor__DO220885_normal	127	64	50.3	16d5519e-ecb9-4fc8-81f1-e0e4adf722a8.embl-delly_1-3-0-preFilter.20150817
DO49445_tumor__DO49445_normal	76	76	100.0	b5cabba2-30a4-458e-897c-00ec3fefa6d2.embl-delly_1-0-0-preFilter.20150622
DO6436_tumor__DO6436_normal	77	77	100.0	ef3b454c-b2cf-4f68-a2ab-733620b6714e.embl-delly_1-0-0-preFilter.20150607
DO51484_tumor__DO51484_normal	142	118	83.0	6ad44218-d34e-4126-bf56-1be2140cd3fb.embl-delly_1-3-0-preFilter.20150826
DO48677_tumor__DO48677_normal	182	151	82.9	9ba2c970-c622-11e3-bf01-24c6515278c0.embl-delly_1-3-0-preFilter.20150829
DO48545_tumor__DO48545_normal	155	155	100.0	44406493-37f4-48c7-961b-8714be50773a.embl-delly_1-0-0-preFilter-hpc.150701
DO51490_tumor__DO51490_normal	159	157	98.7	6297aa77-37a0-4f46-987b-32bd8653c0c2.embl-delly_1-0-0-preFilter.20150722
DO51514_tumor__DO51514_normal	189	188	99.4	65d2dbc3-a163-4696-b246-47a430e66572.embl-delly_1-0-0-preFilter.20150618
DO51187_tumor__DO51187_normal	205	205	100.0	dc7faf84-4438-447b-abcf-a3af87043654.embl-delly_1-0-0-preFilter-hpc.150702
DO220906_tumor__DO220906_normal	249	248	99.5	deb9fbb6-656b-41ce-8299-554efc2379bd.embl-delly_1-0-0-preFilter.20150805
DO51172_tumor__DO51172_normal	273	273	100.0	29127cde-548f-4c42-96cf-6f0020c3db9a.embl-delly_1-0-0-preFilter-hpc.150702
DO34504_tumor__DO34504_normal	275	274	99.6	6bdf00f6-670f-466e-87fb-e853e41f000e.embl-delly_1-0-0-preFilter.20150705
DO49181_tumor__DO49181_normal	294	294	100.0	88bc38ba-ad1d-431e-a67e-0a5a23678386.embl-delly_1-0-0-preFilter-hpc.150701
DO51497_tumor__DO51497_normal	299	299	100.0	a3210fd0-344c-468e-8ff2-2d0869a2fb75.embl-delly_1-0-0-preFilter-hpc.151230
DO49184_tumor__DO49184_normal	303	303	100.0	d4907a1b-8b06-47c5-8bca-c781d9cddaf8.embl-delly_1-0-0-preFilter-hpc.150630
DO51053_tumor__DO51053_normal	378	337	89.1	289790a5-77bd-49a9-a1ec-478a8ecacd7f.embl-delly_1-3-0-preFilter.20150817
DO50427_tumor__DO50427_normal	344	339	98.5	f9c52187-2e82-d58a-e040-11ac0d484fc4.embl-delly_1-0-0-preFilter.20150622
DO51528_tumor__DO51528_normal	341	341	100.0	c0523251-3ac2-4292-bb00-9ae9ea9009f6.embl-delly_1-0-0-preFilter-hpc.150605
DO49076_tumor__DO49076_normal	347	347	100.0	0554ffe5-31f7-43f5-8372-2b73c9cf3527.embl-delly_1-0-0-preFilter-hpc.150630
DO49090_tumor__DO49090_normal	352	352	100.0	4cbe411b-b05e-46bd-bea8-126289a0866c.embl-delly_1-0-0-preFilter-hpc.150630
DO48541_tumor__DO48541_normal	375	375	100.0	5702affd-eafe-42a4-8f56-c1f22f8f184d.embl-delly_1-0-0-preFilter-hpc.150701
DO33488_tumor__DO33488_normal	402	402	100.0	0cf9bbc2-cbd5-4b64-8d90-cfa416307b39.embl-delly_1-0-0-preFilter-hpc.150629
DO45223_tumor__DO45223_normal	425	404	95.0	b67208c4-c622-11e3-bf01-24c6515278c0.embl-delly_1-3-0-preFilter.20150909
DO49129_tumor__DO49129_normal	429	429	100.0	5f94cb62-4019-47ff-bf6a-eeda8e9e033c.embl-delly_1-0-0-preFilter-hpc.150630
DO32875_tumor__DO32875_normal	434	434	100.0	ee5d5e7d-78cf-4a29-a9ee-56aa3da877dd.embl-delly_1-0-0-preFilter-hpc.150628
DO51541_tumor__DO51541_normal	689	487	70.6	3933c60d-73d6-4f74-ae02-fd545fc1f092.embl-delly_1-3-0-preFilter.20150801
DO220841_tumor__DO220841_normal	520	518	99.6	9e0009d1-c993-4247-9706-88ee84591dec.embl-delly_1-0-0-preFilter.20150730
DO45096_tumor__DO45096_normal	522	522	100.0	27fcccdc-c622-11e3-bf01-24c6515278c0.embl-delly_1-0-0-preFilter-hpc.150901
DO51487_tumor__DO51487_normal	681	681	100.0	d333b55b-8bac-4a99-9d23-3cc0c25057bf.embl-delly_1-0-0-preFilter-hpc.151230
DO49460_tumor__DO49460_normal	686	684	99.7	9ffe694e-b488-489e-bdbe-0800e505eec4.embl-delly_1-0-0-preFilter.20150622
DO51466_tumor__DO51466_normal	962	879	91.3	c13fb736-614c-4d5f-83bf-2d7586f4fb53.embl-delly_1-3-0-preFilter.20150826
DO51118_tumor__DO51118_normal	1064	1037	97.4	a6045753-60bb-4e65-bc89-1ef0b47aab35.embl-delly_1-3-0-preFilter.20150816
DO50793_tumor__DO50793_normal	1071	1071	100.0	3f99ae0e-c623-11e3-bf01-24c6515278c0.embl-delly_1-0-0-preFilter-hpc.150901
DO220909_tumor__DO220909_normal	1622	1619	99.8	142b6dbf-c943-4a7d-8ab6-13a975f48d7a.embl-delly_1-0-0-preFilter.20150805
DO45191_tumor__DO45191_normal	9148	9106	99.5	9563a264-c622-11e3-bf01-24c6515278c0.embl-delly_1-0-0-preFilter.20150709