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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
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How to distinguish between INV and BND #100

Open tyyiyi opened 4 years ago

tyyiyi commented 4 years ago

Hi, I am using smoove to call SVs. I want to know why some mutations in the chromosome are INV and some are BND. There are some results, for example:

chr2 29225539 471_1 N N] CHR2: 42271404] 2064.84. SVTYPE = BND; STRANDS = ++: 80; CIPOS = 0,0; CIEND = 0,0; CIPOS95 = 0,0; CIEND95 = 0,0; MATEID = 471_2 ; EVENT = 471; SU = 80; PE = 41; SR = 39; PRPOS = 1; PREND = 1; AC = 1; AN = 4 GT: GQ: SQ: GL: DP: RO: AO: QR: QA: RS: AS: ASC: RP: AP: AB 0/1: 200: 2064.84: -215, -8, -118: 294: 194: 99: 193: 98: 112: 39: 0: 81: 59: 0.34 0 / 0: 200: 0: -0, -74, -247: 248: 248: 0: 247: 0: 138: 0: 0: 109: 0: 0

chr2 42271404 471_2 N N] CHR2: 29225539] 2064.84. SVTYPE = BND; STRANDS = ++: 80; CIPOS = 0,0; CIEND = 0,0; CIPOS95 = 0,0; CIEND95 = 0,0; MATEID = 471_1 ; EVENT = 471; SECONDARY; SU = 80; PE = 41; SR = 39; PRPOS = 1; PREND = 1; AC = 1; AN = 4 GT: GQ: SQ: GL: DP: RO: AO: QR: QA: RS: AS: ASC: RP: AP: AB 0/1: 200: 2064.84: -215, -8, -118: 294: 194: 99: 193: 98: 112: 39: 0: 81: 59: 0.34 0/0: 200: 0: -0, -74, -247: 248: 248: 0: 247: 0: 138: 0: 0: 109: 0: 0

Isn't it an inversion? How does smoove decide that a mutation similar to this is BND instead of INV? And when I used Delly, I encountered this mutation, but it reported INV.

chr2 29225539 INV00001098 G . PASS PRECISE; SVTYPE = INV; SVMETHOD = EMBL.DELLYv0.8.1; CHR2 = chr2; END = 42271405; PE = 60; MAPQ = 60; CT = 3to3; CIPOS = -3,3; CIEND = -3,3; SRMAPQ = 60; INSLEN = 0; HOMLEN = 2; SR = 20; SRQ = 0.995455; CONSENSUS = GGAGTCCCTGGGGCTCTGTGCACTCACCAATCATGATGCCGGAGAAAGCCAGGACCAGGGCGGCCACGAGGGCAGAGGTCACCACAGAGAGGATCAGCGAGAGTGGTAGAGGAAAGGTCCCCTTTTTTGGGTCTCCTTTTAAAATACAGATGGCGAGACCAGCGGCCTGGCGGGCCTGCTGTCCTTGGCAGTGCCTTCTCTACCCTCTTAAATAAAATAA; CE = 1.985; RDRATIO = 0.804132; SOMATIC GT: GL: GQ: FT: RCL: RC: RCR: CN: DR: DV: RR: RV 0/1: -192.382,0, -198.582: 10000: PASS: 407784: 264216: 188845: 1: 71: 60: 61: 60 0/0: 0, -22.5654, -278.288: 10000: PASS: 334062: 279857: 174108: 1: 95: 0: 75: 0

Can you give me some instructions? I'm confused about this. Thank you！ tang

brentp commented 4 years ago

hi, this is more of a question for the lumpy repo as that is what determines the SVTYPE.