I also have another question about the .csv output. When there are 2 SNPs called at the same location, with one as a cons-var and one as a low-freq-var, The coverage is different even though it's at the same position.
the difference in coverage should not be there in newer versions of
LoFreq, e.g. 0.6.1. In older versions coverage was reported after
filtering. There, you might see some variability because there are
different filtering rules for reference and alternate bases. Which
version of LoFreq are you using?
I also have another question about the .csv output. When there are 2 SNPs
called at the same location, with one as a cons-var and one as a
low-freq-var, The coverage is different even though it's at the same
position.
Hello again,
I'm examining the .csv output of the Lofreq snp caller and I noticed an unusual SNP:
linkage_group_10 16337 R>G 0.998987
All other positions have ATCG for the reference, but this one has R. Does that just mean reference? Or is there an N in the reference?
Thanks in advance for your answer!
Hi Jessica,
the reference base ('R') is directly taken from the reference fasta
file that you provided. So there should be an R at that position.
Andreas
On 3 April 2014 05:24, jessica preston jpreston555@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC
I also have another question about the .csv output. When there are 2 SNPs called at the same location, with one as a cons-var and one as a low-freq-var, The coverage is different even though it's at the same position.
eg:
low-freq-var:
linkage_group_10 64910 G>T 0.256705 basecount-A:431;basecount-C:0;basecount-G:151;basecount-T:201;coverage:581
consensus-var:
linkage_group_10 64910 G>A 0.550447 basecount-A:431;basecount-C:0;basecount-G:151;basecount-T:201;coverage:783
Can you explain how the coverage is calculated and why it has two different values at this position?
Thanks a lot!
Hi Jessica,
the difference in coverage should not be there in newer versions of
LoFreq, e.g. 0.6.1. In older versions coverage was reported after
filtering. There, you might see some variability because there are
different filtering rules for reference and alternate bases. Which
version of LoFreq are you using?
Andreas
On 3 April 2014 05:58, jessica preston jpreston555@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC
We are using version 0.6.1. Maybe we will have to calculate allele frequencies using base coverage at each position.