varScan.variants.filter*
I get the following output:
27841 variants
27841 failed to get readcounts for variant allele
0 had read position < 0.1
0 had strandedness < 0.01
0 had var_count < 4
0 had var_freq < 0.05...lt; 0.2
0 passed the strand filter
Apparently, the problem is with obtaining the readcounts.
The bam-readcounts files were …
updated 3.8 years ago • vanessagpds