[Nelsonlab-analysis] 1102 variant calling

[Michael J. C. <mic...@gm...>]

Hi all,

That¹s right, it¹s time for another whole genome sequencing paper by the
Nelson Lab All-Stars!

We have a summary of the SOLiD data here:
https://secure.genome.ucla.edu/index.php/1102_Sequencing#Standard_Libs
I didn¹t personally create those files, but there is a summary about PCR dup
removal on that page. Does anyone know if that was done with samtools or
Picard? If it was Samtools rmdup (and I¹m guessing it was), I want to re-run
it using Picard MarkDuplicates (Samtools misses some percent of the
duplicates, and Picard is really the standard tool for it now).

The processed data is here:
/home/solexa/abi_datasets/Reports/1102_whole_genome_bfast_alignment/
I know there was a variant database created by Brian for 1102 a while back,
but from what I understand the variant database server is gone now. Does
that mean we should re-run the variant calling/queryengine analysis? I want
to get together numbers such as the dbSNP intersect and the coding
consequences and so forth for the whole 1102 data set.
Will the method I used previously to generate queryengine reports (from
here: 
https://secure.genome.ucla.edu/index.php/Sequence_Analysis_HowTo#Step_4_-_Ge
nerating_Reports ) still work?

Thanks,
Mike