Open GoogleCodeExporter opened 9 years ago
[deleted comment]
If I change all the read groups using picard to be closer to what they were
with bamaddrg such that they are:
@RG ID:sample PL:illumina PU:G LB:sample SM:sample
And merge the files using picard such that there are six read groups in two
files, popoolation somehow sees two populations of 20. I had this working just
fine with files with readgroups that were pretty much the same, but done with
bwa samtools instead of bWA GATK.
@RG ID:sample SM:sample
What could possibly be causing popoolation to see two populations of 20?
Original comment by sasig...@ucdavis.edu
on 5 May 2014 at 10:11
And to be clear, the pileup file has 12 samples in it and if you process it
through to vcd in samtools it is how it should be, so its something about the
process of syncing it in popoolation and how it reads the read groups.
Original comment by sasig...@ucdavis.edu
on 6 May 2014 at 1:18
hmm, not sure if i understand your problem.
At no step in pipeline popoolation has to deal with readgroups. i designed it
modulary so read groups should be dealt with, well before you actually start
with popoolation2. the mpileup2sync just translates the mpileup into a more
convenient format but it totally preserves the information of the mpileup. so
thats where read groups are important in the mpileup. I guess this must be a
problem than how you created the mpileup. in the mpluep you should see your two
populations of 6. btw what means 'of 6' is this coverage?
but if you still have the problem please send me a head of your mpileup
Original comment by RoKof...@gmail.com
on 1 Nov 2014 at 7:21
Original issue reported on code.google.com by
sasig...@ucdavis.edu
on 2 May 2014 at 11:59