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tprodanov / parascopy

Copy number estimation and variant calling for duplicated genes using WGS.
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Detection of 1.4 Mb duplication #11

Open wolfgang-braun opened 5 months ago

wolfgang-braun commented 5 months ago

Can parascopy be used to detect larger duplications e.g. a 1.4 Mb in chromosome 17p11.2 based? If so, would 30x fq hg38 data like in this example work?

@E100046761L1C001R00300000033/1
GGACCTAFTTATAGGGTGAGATCTAGGCCTACCTCTGTGATCTCACCCCCCAAACCTCTTCCTGCTGTATTTTCTTTGCAGCACTTATCACTATCTGGAACTATTTACTTTTCTTGTTTATTGTCTGATCTACCACCATTACCGACCCTC
+
GGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGFGGGGGGGFGGGGGFGGGGGGGGGGGGGGFGGGGGGGGGGCFGGFGGGGGGGGFGGGFDCEGGGGGGGGGGGGFGGGGGGCGGGGGGG@GGGCGFFGGFGG:FF@;GEGGG
@E100046761L1C001R00300000044/1
TTTCCTGAGGCAATCCCCAGCCATGTGGAACTGTTAGTAACTTAAACTTCTTTCCTTAAGAAATTATCCAGTCTCAGGAAGTGTGAGAATGGACTAATAAAGTAAATTGGTACTGGTAGAGTGAGTACTGCCACAGAGATAGCCAAAAAC
+
ACEC>ED<A2<FF7CBDBC2?EEC>+@EDAF>EFE>FADDFFADCCFFCDFEBAFFEED@EBEFDE::DBF@F@D?.B?<FCD<6.@6CF85AFB@FD@;;DE>=BB=<E<2F+9@C>>E=@67<@D<F;<2E?A;D71DBA77D/?<D=

Thank you very much!

tprodanov commented 5 months ago

Hi @wolfgang-braun , Thank you for using our tool!

Theoretically, it should not be a problem, but you should try and check what happens. If there are any problems, please write us!