PINDEL -c (chromosome) flag for multiple chromosomes

[opulcy97]

Hi all,

I was wondering whether I can use -c flag in pindel for multiple chromosomes but not ALL. For example: is it possible to choose only chromosome 11 and 20 rather than all chromosomes or NOT running for each chromosome individually?

Thanks in advance.

Regards

[KaiYe]

Hi all,

I was wondering whether I can use -c flag in pindel for multiple chromosomes but not ALL. For example: is it possible to choose only chromosome 11 and 20 rather than all chromosomes or NOT running for each chromosome individually?

Thanks in advance.

Regards

hi,

I am implementing a bed input option. with -j, you can specify which regions to include and with -J which to exclude. half way already. please check out the code (genome/pindel at github) be the end of next week.

Kai

[KaiYe]

Yesterday committed changes to github genome/pindel (https://github.com/genome/pindel). Now -j (include) and -J (exclude) options are available.

Now you can use -c, -j and -J to specify the region of interest/exclude. Pindel first takes -c, -j and -J regions to find out what genomic regions for current run (print the list of regions to screen), then go through each region one by one.

Please let me know whether this is what you needed and do notify me if you find anything strange.

kai