Hi, could someone tell me what is the proper way to run bam-readcount (for later use with the VarScan2 fpfilter.pl?)
Specifically, what should be the "list of regions to report readcounts within" (-l parameter): the SNPs found (from .vcf file)? the exome .bed file?
And how is the "optional region specificaton" different?
An example of a command-line call to bam-readcount would also be useful.
Thank you!
- Elena
Specifically, what should be the "list of regions to report readcounts within" (-l parameter): the SNPs found (from .vcf file)? the exome .bed file?
And how is the "optional region specificaton" different?
An example of a command-line call to bam-readcount would also be useful.
Thank you!
- Elena
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