Question: Galaxy Problem
0
Francesco Vitiello • 30 wrote:
Dear all,
I' really new to the use of Galaxy, NGS analysis and SNP calling.
I have a problem.
After that I generate pileup and filter some reads with the SAMtools
filter
pileup
The resulting data set contain about 2200 SNPs
At least I compare my result data set whit dbSNP132.txt and
1kg.lc.2010_7.CEU.liftedhg19.pgSnp.
The resulting data set contain 700 SNPs.
Now the question:
The problem is that I must have 200 SNPs instead of 700....
I have check the resutls and I saw that some result are duplicated for
all
parameters but had a different rs ID.
how can I remove the wrong one???
please help me.
some one I heard about SOAPsnp but I don't know how to use. Could
anyone
please help me.
Thanks
Francesco
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