Entering edit mode
10.6 years ago
prachi2808
•
0
Hi,
Pindel 0.2.5a1 called the following 2 insertions, in a tumor sample, at the same locus.
7480 I 3 NT 3 "TAA" ChrID chrY BP 13506676 13506677 BP_range 13506676 13506677 Supports 8 7 + 8 7 - 0 0S1 9 SUM_MS 149 1 NumSupSamples 1 1 default 0 0 8 7 0 0
ACGTTCCTTAGAGAGGCTATGGCGTTATTAATCATACCACCTGTAGGGGCACACAAT AAAAAAATTCACAAAGAAATATTTTCACATACACTACACATCAGAAAAGCAAATCTAGGTGGTTCATGAAGAAAAGTAAGCATTTTATAGAA
GGGCAAACAATTAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCAGAAAAGCAAATCTAGGTGGTTCATGAAGAAAAGCAAGCATTTTA + 13506449 17 default @HWI-ST824:289:D18GCACXX:1:1303:15833:87741
GGGGCAAACAATTAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCAGAAAAGCAAATCTAGGTGGTTCATGAAGAAAAGCAAGCATTTT + 13506537 18 default @HWI-ST824:289:D18GCACXX:1:1204:5502:40808
CTGTAGGGGCAAACAATTAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCAGAAAAGCAAATCTAGGTGGTTCATGAAGAAAAGCAAGC + 13506467 17 default @HWI-ST824:289:D18GCACXX:1:1206:19866:98908
ACCACCTGTAGGGGCAAACAATTAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCAGAAAAGCAAATCTAGGTGGTTCATGAAGAAAAG + 13506546 18 default @HWI-ST824:289:D18GCACXX:1:2107:14168:43504
CATACCACCTGTAGGGGCAAACAATTAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCAGAAAAGCAAATCTAGGTGGTTCATGAAGAA + 13506528 17 default @HWI-ST824:289:D18GCACXX:1:1106:2774:116744
TTCCTTACAGAGGCTATGGCGTTATTAAGCATACCACCTGTAGGGGCAAACAATTAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCAG + 13506496 16 default @HWI-ST824:289:D18GCACXX:1:1101:7766:191790
7481 I 4 NT 4 "AAAA" ChrID chrY BP 13506676 13506677 BP_range 13506676 13506684 Supports 4 2 + 4 2 - 0 0S1 5 SUM_MS 59 1 NumSupSamples 1 1 default 0 0 4 2 0 0
ATACGTTCCTTAGAGAGGCTATGGCGTTATTAATCATACCACCTGTAGGGGCACACAAT AAAAAAATTCACAAAGAAATATTTTCACATACACTACACATCAGAAAAGCAAATCTAGGTGGTTCATGAAGAAAAGTAAGCATTTT
GCAAACAATTAAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCAGAAAAGCAAATCTAGGTGGTTCATGAAGAAAAGCAAGCATTTTAT + 13506511 14 default @HWI-ST824:289:D18GCACXX:1:2204:7803:89852
GGCAAACAATTAAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCAGAAAAGCAAATCTAGGTGGTTCATGAAGAAAAGCAAGCATTTTA + 13506464 23 default @HWI-ST824:289:D18GCACXX:1:1307:14920:58485
TTCCTTACAGAGGCTATGGCGTTATTAAGCATACCACCTGTAGGGGCAAACAATTAAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCA + 13506451 12 default @HWI-ST824:289:D18GCACXX:1:1307:18878:91213
TTCCTTACAGAGGCTATGGCGTTATTAAGCATACCACCTGTAGGGGCAAACAATTAAAAAAAAAAATCACAAAGAAATATTTTCACATACACTACACATCA + 13506451 10 default @HWI-ST824:289:D18GCACXX:1:1302:12242:14081
Are these kinds of calls (same locus, different calls) to be treated with caution, or are these valid calls?
Additionally, shouldn't the second call be a TAAA call rather than an AAAA call?
Thanks, Prachi