Confusion about documentation about parameter `-c`

[Steve Huang]

Hi,

I'm reporting a behavior that I was expecting after reading the manual here
http://gmt.genome.wustl.edu/packages/pindel/user-manual.html

-c/--chromosome Which chr/fragment.
Pindel will process reads for one chromosome each time. ChrName must be the same as in reference sequence and in read file. '-c ALL' will make Pindel loop over all chromosomes. The search for indels and SVs can also be limited to a specific region; -c 20:10,000,000 will only look for indels and SVs after position 10,000,000 == [10M, end], -c 20:5,000,000-15,000,000 will report indels in the range between and including the bases at position 5,000,000 and 15,000,000 = [5M, 15M]

It is suggesting that if I specify -c chr1:200000000 (using HG38 human reference), the program should run analysis only from chr1:200000000 till the end of chromosome 1.
But instead I get this error message:

Error, the region end is requested but has not been defined!

Am I misunderstanding things?

Thanks for any clarification!

[Kai Ye]

Please specify a start and an end if -c is applied. The document has not been updated after the change. Sorry for the confusion. Hi, I'm reporting a behavior that I was expecting after reading the manual here http://gmt.genome.wustl.edu/packages/pindel/user-manual.html

…

-c/--chromosome Which chr/fragment. Pindel will process reads for one chromosome each time. ChrName must be the same as in reference sequence and in read file. '-c ALL' will make Pindel loop over all chromosomes. The search for indels and SVs can also be limited to a specific region; -c 20:10,000,000 will only look for indels and SVs after position 10,000,000 == [10M, end], -c 20:5,000,000-15,000,000 will report indels in the range between and including the bases at position 5,000,000 and 15,000,000 = [5M, 15M] It is suggesting that if I specify -c chr1:200000000 (using HG38 human reference), the program should run analysis only from chr1:200000000 till the end of chromosome 1. But instead I get this error message: Error, the region end is requested but has not been defined! Am I misunderstanding things? Thanks for any clarification! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#100>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AB9s-4uRELi2mvy0MM34WoNyaHC2d7Fxks5ucDcYgaJpZM4Ws7u_>.