Chadi Saad

Wrong results when original reads contains soft clipped nucleotides

10

When the original reads contains already soft clipped sequences, final results are wrong, sometimes we have a shift of positions, and some times final reads are shorter then expected

Primers trimming

1

Do V-pipe trim primers ? I can't find the information. (I see only this param in the conf file: primers_file=) If yes, is it done post-alignment ?

Automatically load BAM files

4

Is it possible to load automatically a corresponding BAM file with IGV widget in order to visualize the variant ? Instead of loading it manually each time I open an...

Pisces does not support multi-Mapped reads

3

When having multiple alignement for a same read. In SAM/BAM format, SEQ and QUAL of secondary alignments are set to ‘*’ to reduce the file size. And this cause problems...