I'm using LoFreq to call variants on some human tumor samples. We had analized those samples beforehand, so I had an idea about which variants should be called.
The samples had some variants reported on dbSNP and according to the recommendations in the home page I decided to enable the -s flag and use -S with a dbSNP VCF file, however, those variants weren't being called.
So, I've been wanting to ask: Does the -S option mask/remove the variants on the positions on the file?
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
-S won't mask variants. It just affect the somatic variant quality score.
In fact, adding dbSNP here should have increased the quality of this call.
What happens if you run it without the extra -S? Also, there is not
(lowercase) '-s' option. Was that a typo?
I'm using LoFreq to call variants on some human tumor samples. We had
analized those samples beforehand, so I had an idea about which variants
should be called.
The samples had some variants reported on dbSNP and according to the
recommendations in the home page I decided to enable the -s flag and use -S
with a dbSNP VCF file, however, those variants weren't being called.
So, I've been wanting to ask: Does the -S option mask/remove the variants
on the positions on the file?
I'm running lofreq call to call the variants, not lofreq somatic, and since I'm using human samples, according to the online documentation I should be using -s (source quality) in combination with -S.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
In general, using source quality will give you more conservative calls.
There is a chance that it will undercall in mutational hotspots. Variants
in the "ignore vcf" file are just used to tune the source quality
computation. Normally reads with lots of variants get a low source quality,
however, variants listed in the aforementioned file are ignored for this.
These variants are not used to mask final calls!
I'm running lofreq call to call the variants, not lofreq somatic, and
since I'm using human samples, according to the online documentation I
should be using -s (source quality) in combination with -S.
Thanks for the answers, they are very helpful.
I have a final question, though. Is there a way to check why a possible variant is not being called by LoFreq?
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thanks for the answers, they are very helpful.
I have a final question, though. Is there a way to check why a possible
variant is not being called by LoFreq?
Hello,
I'm using LoFreq to call variants on some human tumor samples. We had analized those samples beforehand, so I had an idea about which variants should be called.
The samples had some variants reported on dbSNP and according to the recommendations in the home page I decided to enable the -s flag and use -S with a dbSNP VCF file, however, those variants weren't being called.
So, I've been wanting to ask: Does the -S option mask/remove the variants on the positions on the file?
Hi Camilo,
-S won't mask variants. It just affect the somatic variant quality score.
In fact, adding dbSNP here should have increased the quality of this call.
What happens if you run it without the extra -S? Also, there is not
(lowercase) '-s' option. Was that a typo?
Best,
Andreas
On 18 May 2018 at 23:13, Camilo cvillaman@users.sourceforge.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC
I'm running lofreq call to call the variants, not lofreq somatic, and since I'm using human samples, according to the online documentation I should be using -s (source quality) in combination with -S.
Oh I see.
In general, using source quality will give you more conservative calls.
There is a chance that it will undercall in mutational hotspots. Variants
in the "ignore vcf" file are just used to tune the source quality
computation. Normally reads with lots of variants get a low source quality,
however, variants listed in the aforementioned file are ignored for this.
These variants are not used to mask final calls!
Hope this answers the question,
Andreas
On 22 May 2018 at 23:14, Camilo cvillaman@users.sourceforge.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC
Thanks for the answers, they are very helpful.
I have a final question, though. Is there a way to check why a possible variant is not being called by LoFreq?
That's only indirectly possible. You can run it with all filters off on the
region of interest:
lofreq call -r sq:start-end --no-default-filter -a 1Andreas
On 23 May 2018 at 11:53, Camilo cvillaman@users.sourceforge.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC
Thanks for the answers.