blastn2snp problem

[mrb20045]

Hi when two or more SNPs are beside each other, blastn2snp reports them in one line like this:

No definition line Homo sapiens chromosome 6, alternate assembly CHM1_1.1 1 9 21 74567818 - TAG ATC 18 A TC TAG .|.

Is it possible blastn2snp reports each snp separately ? I really need it. Thanks

Best

[lindenb]

I'm away from my code: try to change '3' to '2' (or "1" ?) in https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java#L175 and recompile

[mrb20045]

Thanks. I modified the BlastNToSnp.java based on your suggestion and recompiled. But the problem is not fixed. there is another way ?

Best

[lindenb]

I've added a new option -n (int) try to run this tool with -n 0 https://github.com/lindenb/jvarkit/commit/19072426981ab0f13e61755012a4a35da591cc95

[mrb20045]

Dear Pierre Thanks for your great support. the problem is not fixed yet with your improvement. I recompiled and ran the software with -n 0. but in some cases mismatches are reported as two or three like:

1:213087129-213087330(+) gi|229627866 298 1 101 298 + T A 97 T A . 1:213087129-213087330(+) gi|229628918 115 1 101 113 + C A 159 C A . 1:213087129-213087330(+) gi|229630731 7 1 101 262 - TG CT 192 CA AG .. 1:213087129-213087330(+) gi|229631360 26 1 101 200 - TGG CCT 201 CCA AGG ...

Can you fixed the problem please ? Thanks again for your help.

Best

[lindenb]

No, sorry I won't fix this; this is clearly not a SNV but a di/tri nucleotide change. You can always try to remove the lines 204-209 https://github.com/lindenb/jvarkit/blob/19072426981ab0f13e61755012a4a35da591cc95/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java#L204-L209

[mrb20045]

Thanks for your help. I removed the mentioned lines but the problem was not fixed. however i fixed it by my script. Thanks again for your support.

Best