Hello,
Im using Pindel to detect SV's. For the most part I understand the output I am given, but there are a few types I do not. First, Im curious why Im getting some Deletions in my Inversions file, but that is no big deal.
This is a called Inversion
Is this trying to say that the 218 nucleotides between Chr5:131938052-131938271 are inverted? I guess the way the read mapping is displayed I dont see it; I dont get a sense of orientation. Assuming this INV is real and the inverted sequence is represented by the lowercase letters I should, in theory, be able to look up the ref sequence at that position and see the lowercase sequence displayed in reverse order?
The other confusing output is the Large insertion:
Based off of the BP location given, this insertion is only 7nt? That does not seem large. There does not seem to be any other indication of the insert size or sequence. The alignments displayed just looks like poor mapping. Maybe I should just ignore this file altogether.
Does anyone know what to make of these? Thanks.
Im using Pindel to detect SV's. For the most part I understand the output I am given, but there are a few types I do not. First, Im curious why Im getting some Deletions in my Inversions file, but that is no big deal.
This is a called Inversion
Code:
#################################################################################################### 3 INV 218 NT 0:0 "":"" ChrID 5 BP 131938052 131938271 BP_range 131938052 131938271 Supports 5 3 + 1 1 - 4 2 S1 10 SUM_MS 145 1 NumSupSamples 1 1 3498_l5 1 1 4 2 TAAGTTTATAATAAGACTCCTATTAGAGACCAGTTTAATTTATTCTACTGCTTTGTCATACTAATTCAATATAATTTTAAATAAGAATTTGGAATATTTCaaaataaaaattttttaaattacaggaaaaaaaggaaggaagccagccactaagtgaaatgctacatgggtttaaggtacaaaatgtcaacccattttac AGAATTTGGAATATTTCAAAATAAAAATTTTTTAAATTACAGGAAAAAAAGGAAGGAAGCCAGCCACTAAGTGAAATGCTACATGGGTTTAAGGTACAAA + 131938035 29 3498_l5 @HWI-ST628:225:C02ATACXX:5:1203:12456:188553/2 ---------------------------------------------------------------------------------------------------- ctaatgaattaccacctccatggcaggtactgacaactatttttgctgatgcctctgaaacaataatatgtatttaatcttttaaaaaaaatttacttcaGAAATAATGTTAGGATTACAGAAAAATTATAAAAATAATACAAATTATTCATATATATCCCTCATCCAGCTCCTCCTGATGTTAACAATTTATGTACTCT GACAACTATTTTTGCTGATGCCTCTGAAACAATAATATGTATTTAATCTTTTAAAAAAAATTTACTTCAGAAATAATGTTAGGATTACAGAAAAATTATA - 131938301 29 3498_l5 @HWI-ST628:225:C02ATACXX:5:2301:14130:106182/2 GGCAGGTACTGACAACTATTTTTGCTGATGCCTCTGAAACAATAATATGTATTTAATCTTTTAAAAAAAATTTACTTCAGAAATAATGTTAGGATTACAG - 131938291 29 3498_l5 @HWI-ST628:225:C02ATACXX:5:2305:4222:116460/2 GGCAGGTACTGACAACTATTTTTGCTGATGCCTCTGAAACAATAATATGTATTTAATCTTTTAAAAAAAATTTACTTCAGAAATAATGTTAGGATTACAG - 131938291 29 3498_l5 @HWI-ST628:225:C02ATACXX:5:2104:12836:15953/2 GGCAGGTACTGACAACTATTTTTGCTGATGCCTCTGAAACAATAATATGTATTTAATCTTTTAAAAAAAATTTACTTCAGAAATAATGTTAGGATTACAG - 131938291 29 3498_l5 @HWI-ST628:225:C02ATACXX:5:1206:4455:120825/2
The other confusing output is the Large insertion:
Code:
######################################################## 12 LI ChrID 8 90973932 4 90973925 3 TTCAAGGTGAGGAAGTGTGGGAACTATAAAAAATATGGCACACATATTCTGTAGAGAAACTATGTAAAAAAGGCGAGGTCGGGAGGAGGAAGGCTGCAGCtaaactactgaggactcagaagtctagacaaagggcttggagatttattctgtggataataagagctagttaaaatttttgagaaaagagaaggtaattg GCTGCAGCCTTCCTCCTCCCGACCTCGCCTTTTTTACATAGTTTTTCTACAGAATATGTGTGCCATATTTTTTATAGTTCCCACACTTCCTCACCTTGAA GCTGCAGCCTTCCTCCTCCCGACCTCGCCTTTTTTACATAGTTTCTCTACAGAATATGTGTGCCTTATTTTTTATAGTTCCCACACTTCCTCACCTTGAA GCTGCAGCCTTCCTCCTCCCGACCTCGCCTTTTTTACATAGTTTCTCTACAGAATATGTGTGCCCTATTTTTTATAGTTCCCACACTTCCTCACCTTGAA GAACTATAAAAACTATGGCACACATATTCTGTAGAGAAACTATGTAAAAAAGACGAGGTCTGGAGGAGGAAGGGTGCAGCTGAACTACTGAGGTCTCATA -------------------------------------------------------- acatgatgttcaaggtgaggaagtgtgggaactataaaaaatatggcacacatattctgtagagaaactatgtaaaaaaggcgaggtcgggaggaggaagGCTGCAGCTAAACTACTGAGGACTCAGAAGTCTAGACAAAGGGCTTGGAGATTTATTCTGTGGATAATAAGAGCTAGTTAAAATTTTTGAGAAAAGAGAA TTGTCTTTTATCAAAATCTTTAACTAGCTTTTATTATCCACAGAATAAATCTCAAAGCCCTTTGTCTAGTCTTCTGAGTCCTCAGTAGTTTAGCTGCAGC TTCTCTTTTCTCAAAAATTTTAACTAGCTCTTATTGTCCACAGAATAAATTTCCAAGCCCTTTGTCTAGACTTCTGAGTCCTCAGTAGTTTAGCTGCAGC TTCTCTTTTCTCAAAAATTTTGACTAGCTCTTATTATCCACAGAATAAATTTCCAAGCCCTTTGTCTAGACTTCTGAGTCCTCAGTAGTTTAGCTGCAGC
Based off of the BP location given, this insertion is only 7nt? That does not seem large. There does not seem to be any other indication of the insert size or sequence. The alignments displayed just looks like poor mapping. Maybe I should just ignore this file altogether.
Does anyone know what to make of these? Thanks.
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