Length of the output of SVs

[jyw-atgithub]

Hi, I am calling SVs from Drospphila melanogaster with Nanopore sequences. I set the minimal length of SV as 50 (-l 50). But when I viewed the VCF file, it reported any SVs longer than 10bp. May I know how to fix it? The commands and partial results are attached. Thank you! Best,

Jen-Yu

1. commands

cuteSV --threads 20 --genotype \
-l 50 -L 500000 \
-r 500 -q 20 -s 3 \
--max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 \
--sample ${name} \
$j ${ref_genome} "${name}-cutesv.vcf" .

2. result vcf I used "SVLEN" as the length of the length of SV.

2L      149767  cuteSV.DEL.1003 GCCAGCGTCTTCAT  G       0       q5      IMPRECISE;SVTYPE=DEL;SVLEN=-13;END=149780;CIPOS=-26,26;CILEN=-2,2;RE=5;RNAMES=NULL;AF>
2L      150167  cuteSV.DEL.1004 GTTTATAAGTTTT   G       0       q5      IMPRECISE;SVTYPE=DEL;SVLEN=-12;END=150179;CIPOS=-43,43;CILEN=-2,2;RE=4;RNAMES=NULL;AF>
2L      150450  cuteSV.DEL.1005 CGTTAAAATTTAC   C       0       q5      IMPRECISE;SVTYPE=DEL;SVLEN=-12;END=150462;CIPOS=-38,38;CILEN=-2,2;RE=3;RNAMES=NULL;AF>
2L      150742  cuteSV.DEL.1006 GTGCTCGCTTAT    G       0       q5      IMPRECISE;SVTYPE=DEL;SVLEN=-11;END=150753;CIPOS=-78,78;CILEN=-0,0;RE=4;RNAMES=NULL;AF>
2L      151218  cuteSV.DEL.1007 GTTCGACTAATA    G       0       q5      IMPRECISE;SVTYPE=DEL;SVLEN=-11;END=151229;CIPOS=-51,51;CILEN=-1,1;RE=5;RNAMES=NULL;AF>
2L      152093  cuteSV.DEL.1008 TCCCATGTCCAAGCAG        T       0       q5      IMPRECISE;SVTYPE=DEL;SVLEN=-15;END=152108;CIPOS=-93,93;CILEN=-3,3;RE=9;RNAMES>
2L      152609  cuteSV.DEL.1009 GAGAGCTCCTTT    G       0       q5      IMPRECISE;SVTYPE=DEL;SVLEN=-11;END=152620;CIPOS=-53,53;CILEN=-0,0;RE=11;RNAMES=NULL;A>
2L      153226  cuteSV.DEL.1010 CTCGGTCACTT     C       0       q5      IMPRECISE;SVTYPE=DEL;SVLEN=-10;END=153236;CIPOS=-47,47;CILEN=-0,0;RE=5;RNAMES=NULL;AF>
2

3. I used bcftools query and R to organize the lengths

[tjiangHIT]

Hello @jyw-atgithub,

Sorry for replying too late. Could you provide a small bam file covering some cases like these for us in order to reproduce the issue and debug it? I will appreciate it if you can supply it. My email is tjiangAThitDOTeduDOTcn.

Best, Tao

[tjiangHIT]

Hello @jyw-atgithub, Please follow issue #110 to solve this. Best wishes, Tao

[jyw-atgithub]

Hi @tjiangHIT , Thank you for providing the solution. I tried to reinstall the program, but encountered an error. My command was python3 setup.py install --user The following is part of the output. Thank you again.

Downloading https://files.pythonhosted.org/packages/20/b6/36bfb1760f6983788d916096193fc14c83cce512c7787c93380e09458c09/PyVCF-0.6.8.tar.gz#sha256=e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9
Best match: PyVCF 0.6.8
Processing PyVCF-0.6.8.tar.gz
Writing /tmp/easy_install-lpl0dtpr/PyVCF-0.6.8/setup.cfg
Running PyVCF-0.6.8/setup.py -q bdist_egg --dist-dir /tmp/easy_install-lpl0dtpr/PyVCF-0.6.8/egg-dist-tmp-qs5vy87_
error: Setup script exited with error in PyVCF setup command: use_2to3 is invalid.

Environment

OS: Ubuntu 22.04.2 LTS Python 2.7.18 Python 3.10.6

[tjiangHIT]

Hello @jyw-atgithub, Please follow issue #116 to solve this. Best wishes, Tao

[jyw-atgithub]

Hi @tjiangHIT , Thank you very much! cuteSV is installed successfully.

[tjiangHIT]

Hello @jyw-atgithub,

Glad to hear this good news. Is this problem solved through the version of codes in our GitHub? Feel free to contact us.

Best regards, Tao

[jyw-atgithub]

Hi Tao, The problem is resolved. Thank you!