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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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Inversion missed #155

Closed biozzq closed 1 year ago

biozzq commented 1 year ago

Dear @mnshgl0110

If one contig mapped near the center of the chromosome and then split and mapped in reverse orientation to the beginning of the chromosome, it should be a inversion. However, syri missed it in my demo data. I have attached the fasta and BAM files here demo.zip, and the command i used is as follows,

syri -F B -r ref.fa -c demo.bam -q query.fa -k --nosnp --prefix demo

Looking forward to your reply, thanks.

Sincerely,

Zheng zhuqing

mnshgl0110 commented 1 year ago

Syri filters small/low-quality alignment. Using -f stops this filtering and you can find this small inversion.

(mgpy3.8) 11:05 goel@pc-t7-130 netscratch:issue155$ syri -f -F B -r ref.fa -c demo.bam -q query.fa -k --nosnp --prefix demo > garb 2> garb
(mgpy3.8) 11:05 goel@pc-t7-130 netscratch:issue155$ cat demosyri.out
ref 1   70  -   -   query   1   70  INV2    -   INV -
ref 1   70  -   -   query   70  1   INVAL2  INV2    INVAL   -
ref 71  1820    -   -   -   -   -   NOTAL1  -   NOTAL   -
ref 1821    1960    -   -   query   71  210 SYN1    -   SYN -
ref 1821    1960    -   -   query   71  210 SYNAL1  SYN1    SYNAL   -
ref 1961    3290    -   -   -   -   -   NOTAL2  -   NOTAL   -