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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Confusion about documentation about parameter `-c` #100

Open SHuang-Broad opened 6 years ago

SHuang-Broad commented 6 years ago

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!

liangkaiye commented 6 years ago

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!

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