Hi Andreas,
I have used your Lofreq to on my normal/tumor pair to retrieve INDELS. I have only 3 sample pairs for my data and I performed it individually since my tumors have different clonal properties. So I used it on normal/tumor pair and made 3 runs ( one for each pair). I have also used VarScan as well. Now I want to integrate the calls of both VarScan and Lofreq for INDELS and before that I want to use some kind of false positive filtering on the output of Lofreq indel vcf? Is that possible someway? Like we do in VarScan with fpfilter. The fpfilter does not seem to work with Lofreq vcf files. So am asking if there is a way we can filter further the Lofreq vcf files. My idea of project is comparing the genetic background between my 3 sample pairs. Please let me know if my query is clear or not.
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LoFreq results are filtered already relatively stringent (1% p-value
threshold after Bonferroni correction for somatic indels). Why exactly
do you think another filter is necessary? If needed you can filter
results further with the 'lofreq filter' subcommand.
Hi Andreas,
I have used your Lofreq to on my normal/tumor pair to retrieve INDELS. I
have only 3 sample pairs for my data and I performed it individually since
my tumors have different clonal properties. So I used it on normal/tumor
pair and made 3 runs ( one for each pair). I have also used VarScan as well.
Now I want to integrate the calls of both VarScan and Lofreq for INDELS and
before that I want to use some kind of false positive filtering on the
output of Lofreq indel vcf? Is that possible someway? Like we do in VarScan
with fpfilter. The fpfilter does not seem to work with Lofreq vcf files. So
am asking if there is a way we can filter further the Lofreq vcf files. My
idea of project is comparing the genetic background between my 3 sample
pairs. Please let me know if my query is clear or not.
Yes actually I went through the results back and forth and it seems I do not have to do that filtering again. Thanks a lot. The variants seem quite stringently filtered now.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Andreas,
I have used your Lofreq to on my normal/tumor pair to retrieve INDELS. I have only 3 sample pairs for my data and I performed it individually since my tumors have different clonal properties. So I used it on normal/tumor pair and made 3 runs ( one for each pair). I have also used VarScan as well. Now I want to integrate the calls of both VarScan and Lofreq for INDELS and before that I want to use some kind of false positive filtering on the output of Lofreq indel vcf? Is that possible someway? Like we do in VarScan with fpfilter. The fpfilter does not seem to work with Lofreq vcf files. So am asking if there is a way we can filter further the Lofreq vcf files. My idea of project is comparing the genetic background between my 3 sample pairs. Please let me know if my query is clear or not.
Hi Chris,
LoFreq results are filtered already relatively stringent (1% p-value
threshold after Bonferroni correction for somatic indels). Why exactly
do you think another filter is necessary? If needed you can filter
results further with the 'lofreq filter' subcommand.
I hope that answers your question,
Andreas
On 3 March 2015 at 19:21, chris.cornor vd4mmind@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC
Yes actually I went through the results back and forth and it seems I do not have to do that filtering again. Thanks a lot. The variants seem quite stringently filtered now.