Question: Why FS is low when reads aligned from strand seem biased?
0
gravatar for Sharon
12 months ago by
Sharon420
Sharon420 wrote:

Hi Everyone

I wonder why the fisher strand is low whcih means no bias given the number of reads aligned from each strand which show bias? The low coverage is because of the GC content, but why FS is low here?

                       Strand+             Strand-                  FS(FisherStrand)
Sample1 
         Ref              1                        5                            3.5
         Alt              3                       12                                                        
Sample2
         Ref              2                        6                            3.5
         Alt              4                        2  
Sample3
         Ref              2                        8                            3.5        
         Alt              1                        6

Thanks

vcf variant calling exome • 275 views
ADD COMMENTlink modified 12 months ago by finswimmer11k • written 12 months ago by Sharon420
1
gravatar for finswimmer
12 months ago by
finswimmer11k
Germany
finswimmer11k wrote:

The fisher strand test does not describe whether you have significant more reverse or forward reads. It checks whether the ratio between reads having the REF and those having the ALT differ significant between the two strands.

fin swimmer

ADD COMMENTlink written 12 months ago by finswimmer11k

Got it, thanks finswimmer.

ADD REPLYlink written 12 months ago by Sharon420
1

Fine :)

Please mark my answer as accepted if you find it helpful.

fin swimmer

ADD REPLYlink written 12 months ago by finswimmer11k
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