Hi Jen,
Thank you!
It worked on the original BWA, only when it is aligned to hg19 (failed when
the alignment was to hg_g1k_v37.
However, it doen't work on BAM or SAM files after sorting with Select
Matching pattern: XT:A:U
or after filtering the BWA results with Filter SAM on bitwise flag values.
Hello Lilach,
Please try running pileup on the original BWA output - (SAM is an OK
input with this tool) and let us know if you continue to have problems.
Hopefully this helps,
Jen
Galaxy team
//
On 6/14/12 1:36 PM, Lilach Friedman wrote:
Hi,
I am trying to do variants call with "generate
2 matches
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