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TRsv v1.1

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@stat-lab stat-lab released this 20 May 08:25
· 103 commits to main since this release
v1.1
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Learn about vigilant mode.

(1) In TRsv_hifi_v1.1.pl and TRsv_nonhifi_v1.1.pl, a code was added to assign TR-INS to TR regions overlapping normal high-quality < 20 Kb DUPs.
(2) In TRsv_hifi_v1.1.pl and TRsv_nonhifi_v1.1.pl, a code was added to assign TR-DEL to TR regions overlapping normal high-quality < 20 Kb DELs.
(3) Improved estimation of DUP copy number.
(4) Improved genotyping of multiallelic TR-INS or TR-DEL.
(5) The default value of --max_tr_rate was changed from 1.5 to 1.1 for HiFi data (1.2 for non-HiFi data).
(6) The default value of --min_tr_cn was changed from 0.1 to 0.02 for HiFi data.
(7) Fixed bugs in TR-CNV copy number representation in TRsv_hifi_v1.1.pl, TRsv_nonhifi_v1.1.pl and TRsv_joint_call.pl.
(8) The codes in TRsv_hifi_step2.pl and TRsv_nonhifi_step2.pl were modified to improve the detection accuracy of mobile element insertions.
(9) The code in TRsv_step3.pl was modified to shorten runtime in step 3.
(10) The default value of the --overlap_rate option for the TRsv joint_call command was changed from 0.5 to 0.8.
(11) The codes in TRsv_joint_call.pl were modified to improve SV allele classification.

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