Incorrect output

[komalsrathi]

I used the perl script pileup2baseindel.pl on a BAM file for a number of positions and compared the output with my BAM file loaded in IGV. The results from the perl script are incorrect and not consistent with what IGV shows. At some positions the counts are incorrect and at others the base pair.

I checked the perl code, and the problem is not with your logic. The problem is that the variables $chr, $loc and $ref are just parsed once while reading the first line of mpileup. The $chr, $loc and $ref do not change with each line and have a constant value.

[komalsrathi]

I have changed the code and now the program works perfectly well. Let me know if you want me to send it to you so that you can update the code.

[jwendler]

Thank you for this helpful code. The problem with the pileup2baseindel.pl output can be fixed by changing the parsePileup function to include $ref. Otherwise it uses $ref from the wrong scope.

sub parsePileup{
my ($bases,$bq,$BQcut,$offset,$ref) = @_;

Then in the function calls:
my $str = parsePileup($bases,$bq,$BQcut,$offset, $ref);

Cheers,
Jason

[Nitin123-4]

This problem is still there. Still pileup2baseindel.pl is taking wrong ref base.

[chris-aln]

Hi,
I agree with Nitin123-4. The parser is taking the reference base from the first line as the reference base for every following line, when it should be reading a new reference base at each line. I used the updated script from mfoll but it didn't fix this. Does anyone have another version of pileup2base I could look at? :)

[chris-aln]

Hi,
Actually, I just found nordhuang's edit and it works! xD
Thanks.