Indel Size

[Ashini Bolia]

Hi,

I came across SWAN paper today and it looks really good. I wanted to check the indel size range. In the paper it says: 50 -10 kbp. Have you tested it on smaller indels also like 2-50 size range. I understand its for mid-size range indels but just wanted to be sure.

Thanks, Ashini

[Charlie Xia]

Hi,

We didn't focus on that size rangee, but we do see finding indels in the 50bp range in our analysis. You can give it a try on a small chromosome. It wouldn't cost anything.

Best

Charlie

[Charlie Xia]

Not a bug.

[Ashini Bolia]

Hi Charlie,

Thanks for your reply. I am trying SWAN on my data. I was able to install it and the test run went fine. However, when I am trying to use real data, I get this error during the "sclip_scan" stage. I believe this error is due to start > end in my file. I checked online and people suggest flipping start and end.. But I am not sure if that can affect variant calling. Do you have any suggestion or fix for this issue.

Thanks again for all your help.

"Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 2: negative widths are not allowed Calls: IRanges -> solveUserSEW0 -> .Call2 -> .Call Execution halted "

Thanks, Ashini

[Charlie Xia]

Can you narrow it down to a small bam file that this error can be reproduced and send it to me? I will take a look.

[Ashini Bolia]

Hi Charlie, Thanks for getting back to me on this. I think I was able to move past that issue by using "human_g1k_v37.fasta.gap.bed". If I use human_g1k_v37.fasta.gap.txt.gz, I was getting that error, although don't see Start > End in this file at all. Now it passes through the sclip_scan stage but throws another error in the last swan_join stage:

" [1] "Reference/Data/B37/BWA/human_g1k_v37.fasta" ==Info: setting swan file.. ==Info: setting bigd file.. ==Info: setting disc file.. ==Info: parsing par file(s).. Error in file(file, "rt") : cannot open the connection Calls: lapply -> lapply -> FUN -> file Execution halted " Can you suggest what this could be. Thanks. Sorry for bothering you with all these questions and thanks for your patience.

Ashini

[Charlie Xia]

Hi Ashini,

Did you get to pass this point. I was just back from vacation. Let me know.

Best,

Charlie